diff --git a/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java b/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java
index db723ba93bc7156afa8b5bf664e32c3393eb1821..5f8cd1ad4b38b5b28df65cef781e3a5b9932c1c7 100644
--- a/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/geometry/ConversionUtils.java
@@ -42,6 +42,7 @@ public class ConversionUtils
*
* @throws IllegalArgumentException if the location is not a valid one.
*/
+ // TODO 2009-12-16, Tomasz Pylak: x means rows, y means column, it's counterintuitive
public static Point parseSpreadsheetLocation(String spreadsheetLocation)
{
if (spreadsheetLocation == null || spreadsheetLocation.length() == 0)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java
index 0c2ff545e62f0708812b865efdb6f095e0143d67..98e20eedb33225d1ed2483ff74cf259cfa1ecf00 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/GenericMaterialViewer.java
@@ -16,25 +16,16 @@
package ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.material;
-import java.util.Set;
-
import com.extjs.gxt.ui.client.Style.Scroll;
-import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.LayoutContainer;
-import com.extjs.gxt.ui.client.widget.layout.RowData;
import com.google.gwt.user.client.rpc.AsyncCallback;
-import com.google.gwt.user.client.ui.Widget;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientServiceAsync;
/**
@@ -42,101 +33,49 @@ import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.IGenericClientS
*
* @author Piotr Buczek
*/
-abstract public class GenericMaterialViewer extends AbstractViewer<Material> implements
- IDatabaseModificationObserver
+public class GenericMaterialViewer extends AbstractViewer<Material>
{
private static final String PREFIX = "generic-material-viewer_";
public static final String ID_PREFIX = GenericConstants.ID_PREFIX + PREFIX;
- abstract protected void getMaterialInfo(final AsyncCallback<Material> materialInfoCallback);
-
- private final IViewContext<?> viewContext;
-
- protected final TechId materialId;
-
public static DatabaseModificationAwareComponent create(
final IViewContext<IGenericClientServiceAsync> viewContext, final TechId materialId)
{
- GenericMaterialViewer viewer = new GenericMaterialViewer(viewContext, materialId)
- {
- @Override
- protected void getMaterialInfo(AsyncCallback<Material> materialInfoCallback)
- {
- viewContext.getService().getMaterialInfo(materialId, materialInfoCallback);
- }
- };
- viewer.reloadData();
- return new DatabaseModificationAwareComponent(viewer, viewer);
+
+ final GenericMaterialViewer viewer = new GenericMaterialViewer(viewContext, materialId);
+ MaterialPropertiesComponent propsComp =
+ new MaterialPropertiesComponent(viewContext, materialId, -1, -1)
+ {
+ @Override
+ protected void getMaterialInfo(
+ final AsyncCallback<Material> materialInfoCallback)
+ {
+ AbstractAsyncCallback<Material> callback =
+ new AbstractAsyncCallback<Material>(viewContext)
+ {
+ @Override
+ protected void process(Material result)
+ {
+ viewer.updateOriginalData(result);
+ materialInfoCallback.onSuccess(result);
+ }
+ };
+ viewContext.getService().getMaterialInfo(materialId, callback);
+ }
+ };
+ viewer.add(propsComp);
+ return new DatabaseModificationAwareComponent(viewer, propsComp);
}
protected GenericMaterialViewer(final IViewContext<?> viewContext, final TechId materialId)
{
super(viewContext, createId(materialId));
- this.materialId = materialId;
- this.viewContext = viewContext;
+ setScrollMode(Scroll.AUTO);
}
public static String createId(final TechId materialId)
{
return ID_PREFIX + materialId;
}
-
- private static void addSection(final LayoutContainer lc, final Widget w)
- {
- lc.add(w, new RowData(-1, -1, new Margins(5)));
- }
-
- /**
- * Load the material information.
- */
- protected void reloadData()
- {
- getMaterialInfo(new MaterialInfoCallback(viewContext, this));
- }
-
- private static final class MaterialInfoCallback extends AbstractAsyncCallback<Material>
- {
- private final GenericMaterialViewer genericMaterialViewer;
-
- private MaterialInfoCallback(final IViewContext<?> viewContext,
- final GenericMaterialViewer viewer)
- {
- super(viewContext);
- this.genericMaterialViewer = viewer;
- }
-
- /**
- * Sets the {@link Material} for this <var>generic</var> material viewer.
- * <p>
- * This method triggers the whole <i>GUI</i> construction.
- * </p>
- */
- @Override
- protected final void process(final Material result)
- {
- genericMaterialViewer.updateOriginalData(result);
- genericMaterialViewer.removeAll();
- genericMaterialViewer.setScrollMode(Scroll.AUTO);
- addSection(genericMaterialViewer, new MaterialPropertiesSection(result, viewContext));
- genericMaterialViewer.layout();
- }
-
- }
-
- public DatabaseModificationKind[] getRelevantModifications()
- {
- return new DatabaseModificationKind[]
- { DatabaseModificationKind.edit(ObjectKind.MATERIAL),
- DatabaseModificationKind.createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- DatabaseModificationKind.edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
- DatabaseModificationKind.createOrDelete(ObjectKind.VOCABULARY_TERM),
- DatabaseModificationKind.edit(ObjectKind.VOCABULARY_TERM) };
- }
-
- public void update(Set<DatabaseModificationKind> observedModifications)
- {
- reloadData(); // reloads everything
- }
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/MaterialPropertiesComponent.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/MaterialPropertiesComponent.java
new file mode 100644
index 0000000000000000000000000000000000000000..487c6d510f3ae3a9697e197d2c4aa925a3ba703c
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/material/MaterialPropertiesComponent.java
@@ -0,0 +1,115 @@
+/*
+ * Copyright 2009 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.generic.client.web.client.application.material;
+
+import java.util.Set;
+
+import com.extjs.gxt.ui.client.util.Margins;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+import com.google.gwt.user.client.rpc.AsyncCallback;
+import com.google.gwt.user.client.ui.Widget;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
+
+/**
+ * @author Tomasz Pylak
+ */
+abstract public class MaterialPropertiesComponent extends LayoutContainer implements
+ IDatabaseModificationObserver
+{
+ abstract protected void getMaterialInfo(final AsyncCallback<Material> materialInfoCallback);
+
+ private final IViewContext<?> viewContext;
+
+ protected final TechId materialId;
+
+ private final int width;
+
+ private final int height;
+
+ protected MaterialPropertiesComponent(final IViewContext<?> viewContext,
+ final TechId materialId, int width, int height)
+ {
+ this.materialId = materialId;
+ this.viewContext = viewContext;
+ this.width = width;
+ this.height = height;
+ reloadData();
+ }
+
+ private void addSection(final LayoutContainer lc, final Widget w)
+ {
+ lc.add(w, new RowData(width, height, new Margins(5)));
+ }
+
+ /**
+ * Load the material information.
+ */
+ protected void reloadData()
+ {
+ getMaterialInfo(new MaterialInfoCallback(viewContext, this));
+ }
+
+ private final class MaterialInfoCallback extends AbstractAsyncCallback<Material>
+ {
+ private final MaterialPropertiesComponent viewer;
+
+ private MaterialInfoCallback(final IViewContext<?> viewContext,
+ final MaterialPropertiesComponent viewer)
+ {
+ super(viewContext);
+ this.viewer = viewer;
+ }
+
+ /**
+ * Sets the {@link Material} for this <var>generic</var> material viewer.
+ * <p>
+ * This method triggers the whole <i>GUI</i> construction.
+ * </p>
+ */
+ @Override
+ protected final void process(final Material result)
+ {
+ viewer.removeAll();
+ addSection(viewer, new MaterialPropertiesSection(result, viewContext));
+ viewer.layout();
+ }
+
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[]
+ { DatabaseModificationKind.edit(ObjectKind.MATERIAL),
+ DatabaseModificationKind.createOrDelete(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ DatabaseModificationKind.edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT),
+ DatabaseModificationKind.createOrDelete(ObjectKind.VOCABULARY_TERM),
+ DatabaseModificationKind.edit(ObjectKind.VOCABULARY_TERM) };
+ }
+
+ public void update(Set<DatabaseModificationKind> observedModifications)
+ {
+ reloadData(); // reloads everything
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java
index fa1af0a3785215e6e08509fb7f38af829fb4878d..b3632ddc041dea55167db1e31ee7078dde1ad5d3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningImageReportingPlugin.java
@@ -40,7 +40,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImage;
/**
* Reporting plugin which shows all images in wells of a plate dataset.
@@ -50,6 +49,22 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImage;
public class ScreeningImageReportingPlugin extends AbstractDatastorePlugin implements
IReportingPluginTask
{
+ // -------- column headers used to describe images for a plate ------
+
+ private static final String IMAGE = "Thumbnail";
+
+ private static final String CHANNEL = "Channel";
+
+ private static final String TILE = "Tile";
+
+ private static final String COLUMN = "Column";
+
+ private static final String ROW = "Row";
+
+ private static final String DATASET_CODE = "Dataset Code";
+
+ // ----------
+
private static final long serialVersionUID = 1L;
public ScreeningImageReportingPlugin(Properties properties, File storeRoot)
@@ -75,12 +90,12 @@ public class ScreeningImageReportingPlugin extends AbstractDatastorePlugin imple
private void addReportHeaders(SimpleTableModelBuilder builder)
{
// Note: we rely on that column order at the openBIS server side!
- builder.addHeader(PlateImage.DATASET_CODE);
- builder.addHeader(PlateImage.ROW);
- builder.addHeader(PlateImage.COLUMN);
- builder.addHeader(PlateImage.TILE);
- builder.addHeader(PlateImage.CHANNEL);
- builder.addHeader(PlateImage.IMAGE);
+ builder.addHeader(DATASET_CODE);
+ builder.addHeader(ROW);
+ builder.addHeader(COLUMN);
+ builder.addHeader(TILE);
+ builder.addHeader(CHANNEL);
+ builder.addHeader(IMAGE);
}
private void addReportRows(SimpleTableModelBuilder builder, DatasetDescription dataset,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
index 27b3c39914ea453eef2397b17e6831521e8c3e70..a66f64f85dd36f4552c8064b63346fa40495af51 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
@@ -31,9 +31,9 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPlugi
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
/**
* Reporting plugin which shows parameters of the images acquired for a plate dataset.
@@ -43,6 +43,22 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImagePara
public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastorePlugin implements
IReportingPluginTask
{
+ // -------- column headers used in a DSS service to describe images for a plate ------
+
+ private static final String DATASET = "Dataset";
+
+ private static final String ROWS = "Rows";
+
+ private static final String COLUMNS = "Columns";
+
+ private static final String TILE_ROWS_NUM = "Tile rows";
+
+ private static final String TILE_COLS_NUM = "Tile columns";
+
+ private static final String CHANNELS_NUM = "Number of channels";
+
+ // ----------
+
private static final long serialVersionUID = 1L;
public ScreeningPlateImageParamsReportingPlugin(Properties properties, File storeRoot)
@@ -68,11 +84,12 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
private void addReportHeaders(SimpleTableModelBuilder builder)
{
// Note: we rely on that column order at the openBIS server side!
- builder.addHeader(PlateImageParameters.ROWS);
- builder.addHeader(PlateImageParameters.COLUMNS);
- builder.addHeader(PlateImageParameters.TILE_ROWS_NUM);
- builder.addHeader(PlateImageParameters.TILE_COLS_NUM);
- builder.addHeader(PlateImageParameters.CHANNELS_NUM);
+ builder.addHeader(DATASET);
+ builder.addHeader(ROWS);
+ builder.addHeader(COLUMNS);
+ builder.addHeader(TILE_ROWS_NUM);
+ builder.addHeader(TILE_COLS_NUM);
+ builder.addHeader(CHANNELS_NUM);
}
private void addReportRows(SimpleTableModelBuilder builder, DatasetDescription dataset,
@@ -82,12 +99,18 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
Geometry wellGeometry = imageAccessor.getWellGeometry();
int channels = imageAccessor.getChannelCount();
List<ISerializableComparable> row =
- Arrays.<ISerializableComparable> asList(asNum(plateGeometry.getRows()),
- asNum(plateGeometry.getColumns()), asNum(wellGeometry.getRows()),
- asNum(wellGeometry.getColumns()), asNum(channels));
+ Arrays.<ISerializableComparable> asList(asText(dataset.getDatasetCode()),
+ asNum(plateGeometry.getRows()), asNum(plateGeometry.getColumns()),
+ asNum(wellGeometry.getRows()), asNum(wellGeometry.getColumns()),
+ asNum(channels));
builder.addRow(row);
}
+ private static ISerializableComparable asText(String text)
+ {
+ return new StringTableCell(text);
+ }
+
private static ISerializableComparable asNum(int num)
{
return new IntegerTableCell(num);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/geneviewer/ScreeningGeneViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/geneviewer/ScreeningGeneViewer.java
index 72c9a9c365907e5a276927a349807c8ba7f4ed4a..0609b1ce7dd37ed4925501646555540c9fc7b7be 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/geneviewer/ScreeningGeneViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/geneviewer/ScreeningGeneViewer.java
@@ -16,41 +16,174 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.geneviewer;
+import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.utils.GuiUtils.withLabel;
+
+import java.util.List;
+
+import com.extjs.gxt.ui.client.Style.Scroll;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.Text;
+import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
+import com.extjs.gxt.ui.client.widget.layout.RowLayout;
+import com.extjs.gxt.ui.client.widget.layout.TableData;
+import com.extjs.gxt.ui.client.widget.layout.TableLayout;
+import com.google.gwt.event.dom.client.ClickHandler;
import com.google.gwt.user.client.rpc.AsyncCallback;
+import com.google.gwt.user.client.ui.Widget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.AbstractViewer;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.IChosenEntityListener;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField.ExperimentChooserFieldAdaptor;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.listener.OpenEntityDetailsTabClickListener;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityReference;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.material.GenericMaterialViewer;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.material.MaterialPropertiesComponent;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.plateviewer.WellContentDialog;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.plateviewer.WellImages;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.utils.GuiUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImages;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
/**
* @author Tomasz Pylak
*/
-public class ScreeningGeneViewer extends GenericMaterialViewer
+public class ScreeningGeneViewer extends AbstractViewer<Material>
{
+ private static final String PREFIX = GenericConstants.ID_PREFIX + "ScreeningGeneViewer_";
+
public static DatabaseModificationAwareComponent create(
final IViewContext<IScreeningClientServiceAsync> viewContext, final TechId materialId)
{
ScreeningGeneViewer viewer = new ScreeningGeneViewer(viewContext, materialId);
- viewer.reloadData();
- return new DatabaseModificationAwareComponent(viewer, viewer);
+
+ return new DatabaseModificationAwareComponent(viewer, viewer.propertiesSection);
}
private final IViewContext<IScreeningClientServiceAsync> viewContext;
- protected ScreeningGeneViewer(IViewContext<IScreeningClientServiceAsync> viewContext,
- TechId materialId)
+ private final MaterialPropertiesComponent propertiesSection;
+
+ protected ScreeningGeneViewer(final IViewContext<IScreeningClientServiceAsync> viewContext,
+ final TechId materialId)
{
- super(viewContext, materialId);
+ super(viewContext, createId(materialId));
+ this.propertiesSection = new MaterialPropertiesComponent(viewContext, materialId, -1, 1)
+ {
+ @Override
+ protected void getMaterialInfo(AsyncCallback<Material> materialInfoCallback)
+ {
+ viewContext.getService().getMaterialInfo(materialId, materialInfoCallback);
+ }
+ };
this.viewContext = viewContext;
+ setLayout(new BorderLayout());
+ add(propertiesSection, createLeftBorderLayoutData());
+ add(createLocationsPanel(materialId), createRightBorderLayoutData());
+ }
+
+ private Widget createLocationsPanel(final TechId materialId)
+ {
+ final LayoutContainer container = new LayoutContainer();
+
+ ExperimentChooserFieldAdaptor experimentChooser =
+ ExperimentChooserField.create("", true, null, viewContext.getCommonViewContext());
+ ExperimentChooserField chooserField = experimentChooser.getChooserField();
+ chooserField.addChosenEntityListener(new IChosenEntityListener<Experiment>()
+ {
+ public void entityChosen(Experiment entity)
+ {
+ if (entity != null)
+ {
+ loadGeneLocationsPanel(materialId, entity, container);
+ }
+ }
+ });
+ chooserField.setEditable(false);
+ container.add(GuiUtils.withLabel(experimentChooser.getField(), "Experiment:"));
+ container.add(new Text(
+ "Choose an experiment to find wells where this gene has been suppressed."));
+ return container;
}
- @Override
- protected void getMaterialInfo(AsyncCallback<Material> materialInfoCallback)
+ private void loadGeneLocationsPanel(TechId materialId, Experiment entity,
+ final LayoutContainer container)
{
- viewContext.getService().getMaterialInfo(materialId, materialInfoCallback);
+ GuiUtils
+ .replaceLastItem(container, new Text(viewContext.getMessage(Dict.LOAD_IN_PROGRESS)));
+ viewContext.getService().getPlateLocations(materialId,
+ new ExperimentIdentifier(entity.getIdentifier()),
+ new AbstractAsyncCallback<List<WellLocation>>(viewContext)
+ {
+ @Override
+ protected void process(List<WellLocation> wellLocations)
+ {
+ Widget geneLocationsPanel = createGeneLocationPanel(wellLocations);
+ GuiUtils.replaceLastItem(container, geneLocationsPanel);
+ }
+ });
}
+ private Widget createGeneLocationPanel(List<WellLocation> wellLocations)
+ {
+ LayoutContainer container = new LayoutContainer();
+ container.setScrollMode(Scroll.AUTO);
+ container.setLayout(new TableLayout(3));
+ TableData cellLayout = new TableData();
+ cellLayout.setPadding(20);
+ for (WellLocation loc : wellLocations)
+ {
+ container.add(createLocationDescription(loc), cellLayout);
+ }
+ return container;
+ }
+
+ private LayoutContainer createLocationDescription(WellLocation loc)
+ {
+ LayoutContainer container = new LayoutContainer();
+ container.setLayout(new RowLayout());
+ int margin = 4;
+
+ Widget plateLink = createEntityLink(loc.getPlate());
+ container.add(withLabel(plateLink, "Plate: ", margin));
+
+ Widget wellLink = createEntityLink(loc.getWell());
+ container.add(withLabel(wellLink, "Well: ", margin));
+
+ Widget contentLink = createEntityLink(loc.getMaterialContent());
+ container.add(withLabel(contentLink, "Content: ", margin));
+
+ if (loc.tryGetImages() != null)
+ {
+ container.add(createImageViewer(loc.tryGetImages()));
+ }
+ return container;
+ }
+
+ private Widget createImageViewer(TileImages images)
+ {
+ WellImages wellImages = new WellImages(images);
+ return WellContentDialog.createImageViewer(wellImages, viewContext, 100, 60);
+ }
+
+ private Widget createEntityLink(EntityReference entity)
+ {
+ final ClickHandler listener = new OpenEntityDetailsTabClickListener(entity, viewContext);
+ return LinkRenderer.getLinkWidget(entity.getCode(), listener);
+ }
+
+ public static final String createId(final TechId materialId)
+ {
+ return PREFIX + materialId;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateContentGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateContentGrid.java
new file mode 100644
index 0000000000000000000000000000000000000000..ac8f706932e0643851187689dde67dda8ae17a6d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateContentGrid.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright 2009 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.plateviewer;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IColumnDefinition;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class PlateContentGrid extends AbstractSimpleBrowserGrid<WellData>
+{
+
+ protected PlateContentGrid(IViewContext<ICommonClientServiceAsync> viewContext,
+ String browserId, String gridId, IDisplayTypeIDGenerator displayTypeIDGenerator)
+ {
+ super(viewContext, browserId, gridId, true, displayTypeIDGenerator);
+ // TODO Auto-generated constructor stub
+ }
+
+ @Override
+ protected IColumnDefinitionKind<WellData>[] getStaticColumnsDefinition()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected List<IColumnDefinition<WellData>> getInitialFilters()
+ {
+ return new ArrayList<IColumnDefinition<WellData>>();
+ }
+
+ @Override
+ protected void listEntities(DefaultResultSetConfig<String, WellData> resultSetConfig,
+ AbstractAsyncCallback<ResultSet<WellData>> callback)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ protected void prepareExportEntities(TableExportCriteria<WellData> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[] {};
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateLayoutSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateLayoutSection.java
index 9e157cab35392d11f20d170a1c4175dd66688b40..a5604c8eef2e061c571dbd4fb4085767639eccf9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateLayoutSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/PlateLayoutSection.java
@@ -52,8 +52,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.ScreeningCons
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImage;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImage;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
@@ -293,7 +293,7 @@ public class PlateLayoutSection extends SingleSectionPanel
{
public void handleEvent(BaseEvent ce)
{
- WellContentDialog.show(wellData, plateContent, viewContext);
+ WellContentDialog.showContentDialog(wellData, viewContext);
}
});
widget.sinkEvents(Events.OnMouseDown.getEventCode());
@@ -371,7 +371,7 @@ public class PlateLayoutSection extends SingleSectionPanel
{
WellData[][] matrix =
new WellData[plateContent.getRowsNum() + 1][plateContent.getColsNum() + 1];
- PlateImages plateImages = plateContent.tryGetImages();
+ TileImages plateImages = plateContent.tryGetImages();
if (plateImages != null)
{
addImagePaths(plateContent, matrix, plateImages.getImages());
@@ -391,7 +391,7 @@ public class PlateLayoutSection extends SingleSectionPanel
WellData wellData = matrix[row][col];
if (wellData == null)
{
- wellData = new WellData(plateContent);
+ wellData = WellData.create(plateContent);
matrix[row][col] = wellData;
}
wellData.setMetadata(well);
@@ -399,16 +399,16 @@ public class PlateLayoutSection extends SingleSectionPanel
}
private static void addImagePaths(PlateContent plateContent, WellData[][] matrix,
- List<PlateImage> imagesList)
+ List<TileImage> imagesList)
{
- for (PlateImage image : imagesList)
+ for (TileImage image : imagesList)
{
int row = image.getRow();
int col = image.getColumn();
WellData wellData = matrix[row][col];
if (wellData == null)
{
- wellData = new WellData(plateContent);
+ wellData = WellData.create(plateContent);
matrix[row][col] = wellData;
}
wellData.addImage(image);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellContentDialog.java
index cbbac1e036fe6c1bf2e8b8d107864e8d4cd79f25..27bc15be66cc6794627cb1e1ab9668218d8e7e7c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellContentDialog.java
@@ -45,9 +45,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.listene
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.utils.GuiUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
@@ -57,40 +55,54 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
*/
public class WellContentDialog
{
- private static final int TILE_IMG_WIDTH = 200;
-
- private static final int TILE_IMG_HEIGHT = 120;
-
- private final WellData wellData;
-
- private final PlateContent plateContent;
+ private final WellMetadata metadataOrNull;
private final IViewContext<?> viewContext;
- public static void show(final WellData wellData, final PlateContent plateContent,
- final IViewContext<?> viewContext)
+ public static void showContentDialog(final WellData wellData, final IViewContext<?> viewContext)
{
final LayoutContainer container = new LayoutContainer();
container.setLayout(new RowLayout());
- final WellContentDialog viewer = new WellContentDialog(wellData, plateContent, viewContext);
- LayoutContainer descriptionContainer = viewer.createContentDescription();
+ final WellContentDialog contentDialog =
+ new WellContentDialog(wellData.tryGetMetadata(), viewContext);
+ LayoutContainer descriptionContainer = contentDialog.createContentDescription();
container.add(descriptionContainer);
int dialogWidth;
int dialogHeight;
- PlateImages images = plateContent.tryGetImages();
+
+ final WellImages images = wellData.tryGetImages();
if (images != null)
{
- PlateImageParameters imageParameters = images.getImageParameters();
- final int tileRowsNum = imageParameters.getTileRowsNum();
- final int tileColsNum = imageParameters.getTileColsNum();
- int channelsNum = imageParameters.getChannelsNum();
+ int imgW = 200;
+ int imgH = 120;
+ LayoutContainer imageViewer = createImageViewer(images, viewContext, imgW, imgH);
+ container.add(imageViewer);
+
+ dialogWidth = imgW * images.getTileColsNum();
+ dialogHeight = imgH * images.getTileRowsNum() + 160;
+ } else
+ {
+ dialogWidth = 250;
+ dialogHeight = 160;
+ }
+ String title = "Well Content: " + wellData.getWellSubcode();
+ showWellContentDialog(container, dialogWidth, dialogHeight, title);
+ }
- final List<String> channelNames = createChannelsDescriptions(channelsNum);
+ public static LayoutContainer createImageViewer(final WellImages images,
+ final IViewContext<?> viewContext, final int imageWidth, final int imageHeight)
+ {
+ final LayoutContainer container = new LayoutContainer();
+ container.setLayout(new RowLayout());
+
+ int channelsNum = images.getChannelsNum();
+
+ final List<String> channelNames = createChannelsDescriptions(channelsNum);
+ if (channelsNum > 1)
+ {
ComboBox<SimpleComboValue<String>> channelChooser = createChannelChooser(channelNames);
- descriptionContainer.add(new Text("Channel:"));
- descriptionContainer.add(channelChooser);
channelChooser
.addSelectionChangedListener(new SelectionChangedListener<SimpleComboValue<String>>()
{
@@ -101,25 +113,17 @@ public class WellContentDialog
String value = se.getSelectedItem().getValue();
int channel = channelNames.indexOf(value) + 1;
LayoutContainer wellsGrid =
- viewer.createWellsGrid(tileRowsNum, tileColsNum, channel);
- int lastItemIx = container.getItemCount() - 1;
- container.remove(container.getWidget(lastItemIx));
- container.insert(wellsGrid, lastItemIx);
- container.layout();
+ createWellsGrid(images, channel, viewContext, imageWidth,
+ imageHeight);
+ GuiUtils.replaceLastItem(container, wellsGrid);
}
});
- LayoutContainer wellsGrid = viewer.createWellsGrid(tileRowsNum, tileColsNum, 1);
- container.add(wellsGrid);
-
- dialogWidth = TILE_IMG_WIDTH * tileColsNum;
- dialogHeight = TILE_IMG_HEIGHT * tileRowsNum + 160;
- } else
- {
- dialogWidth = 250;
- dialogHeight = 160;
+ container.add(GuiUtils.withLabel(channelChooser, "Channel:"));
}
- String title = "Well Content: " + wellData.getWellSubcode();
- showWellContentDialog(container, dialogWidth, dialogHeight, title);
+ LayoutContainer wellsGrid =
+ createWellsGrid(images, 1, viewContext, imageWidth, imageHeight);
+ container.add(wellsGrid);
+ return container;
}
private static ComboBox<SimpleComboValue<String>> createChannelChooser(List<String> channelNames)
@@ -158,19 +162,18 @@ public class WellContentDialog
container.setLayout(tableLayout);
TableData cellLayout = new TableData();
cellLayout.setMargin(2);
- WellMetadata metadata = wellData.tryGetMetadata();
- if (metadata != null)
+ if (metadataOrNull != null)
{
container.add(new Text("Well: "), cellLayout);
- container.add(createEntityLink(metadata.getWellSample()));
+ container.add(createEntityLink(metadataOrNull.getWellSample()));
- Material content = metadata.tryGetContent();
+ Material content = metadataOrNull.tryGetContent();
if (content != null)
{
container.add(new Text("Content: "), cellLayout);
container.add(createEntityLink(content));
- Material gene = metadata.tryGetGene();
+ Material gene = metadataOrNull.tryGetGene();
if (gene != null)
{
container.add(new Text("Inhibited gene: "), cellLayout);
@@ -199,35 +202,32 @@ public class WellContentDialog
return LinkRenderer.getLinkWidget(entity.getCode(), listener);
}
- private WellContentDialog(WellData wellData, PlateContent plateContent,
- IViewContext<?> viewContext)
+ private WellContentDialog(WellMetadata metadataOrNull, IViewContext<?> viewContext)
{
- this.wellData = wellData;
- this.plateContent = plateContent;
+ this.metadataOrNull = metadataOrNull;
this.viewContext = viewContext;
}
- private LayoutContainer createWellsGrid(int tileRowsNum, int tileColsNum, int channel)
+ private static LayoutContainer createWellsGrid(WellImages images, int channel,
+ IViewContext<?> viewContext, int imageWidth, int imageHeight)
{
- LayoutContainer container = new LayoutContainer(new TableLayout(tileColsNum));
- for (int i = 1; i <= tileRowsNum * tileColsNum; i++)
+ LayoutContainer container = new LayoutContainer(new TableLayout(images.getTileColsNum()));
+ for (int i = 1; i <= images.getTileRowsNum() * images.getTileColsNum(); i++)
{
Component tileContent;
- String imagePath = wellData.tryGetImagePath(channel, i);
+ String imagePath = images.tryGetImagePath(channel, i);
if (imagePath != null)
{
- // if we have a path, then download URL should be also available
- String downloadUrl = plateContent.tryGetImages().getDownloadUrl();
String sessionId = getSessionId(viewContext);
String imageURL =
- SimpleDatastoreImageRenderer.createDatastoreImageUrl(imagePath,
- TILE_IMG_WIDTH, TILE_IMG_HEIGHT, downloadUrl, sessionId);
+ SimpleDatastoreImageRenderer.createDatastoreImageUrl(imagePath, imageWidth,
+ imageHeight, images.getDownloadUrl(), sessionId);
tileContent = new Html(imageURL);
PlateStyleSetter.setPointerCursor(tileContent);
} else
{
tileContent = new Text("No image.");
- tileContent.setPixelSize(TILE_IMG_WIDTH, TILE_IMG_HEIGHT);
+ tileContent.setPixelSize(imageWidth, imageHeight);
}
container.add(tileContent);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellData.java
index fb7f283d41645df122965fa951091925847f7046..7171ab97ff0e9b3e6d68de201d033b192938c90c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellData.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellData.java
@@ -17,9 +17,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.plateviewer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImage;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImage;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
@@ -29,35 +28,26 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
*/
class WellData
{
- private String[/* channel */][/* tile number */] imagePaths;
-
private WellMetadata metadata;
- public WellData(PlateContent plateContent)
+ private WellImages imagesOrNull;
+
+ public static WellData create(PlateContent plateContent)
{
- PlateImages images = plateContent.tryGetImages();
+ TileImages images = plateContent.tryGetImages();
if (images != null)
{
- this.imagePaths = initImagePathArray(images.getImageParameters());
+ return new WellData(
+ new WellImages(images.getImageParameters(), images.getDownloadUrl()));
} else
{
- this.imagePaths = null;
+ return new WellData(null);
}
}
- private String[][] initImagePathArray(PlateImageParameters params)
- {
- int tilesNum = params.getTileRowsNum() * params.getTileColsNum();
- return new String[params.getChannelsNum()][tilesNum];
- }
-
- public void addImage(PlateImage image)
+ private WellData(WellImages imagesOrNull)
{
- int channelIx = image.getChannel() - 1;
- int tileIx = image.getTile() - 1;
- assert imagePaths != null && imagePaths[channelIx][tileIx] == null : "duplicated image for channelIx = "
- + channelIx + ", tileIx = " + tileIx;
- imagePaths[channelIx][tileIx] = image.getImagePath();
+ this.imagesOrNull = imagesOrNull;
}
public void setMetadata(WellMetadata well)
@@ -65,11 +55,6 @@ class WellData
this.metadata = well;
}
- public String tryGetImagePath(int channel, int tile)
- {
- return imagePaths != null ? imagePaths[channel - 1][tile - 1] : null;
- }
-
public WellMetadata tryGetMetadata()
{
return metadata;
@@ -96,4 +81,20 @@ class WellData
return "?";
}
}
+
+ public WellImages tryGetImages()
+ {
+ return imagesOrNull;
+ }
+
+ public void addImage(TileImage image)
+ {
+ assert imagesOrNull != null;
+ imagesOrNull.addImage(image);
+ }
+
+ public String tryGetImagePath(int channel, int tile)
+ {
+ return imagesOrNull == null ? null : imagesOrNull.tryGetImagePath(channel, tile);
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellImages.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellImages.java
new file mode 100644
index 0000000000000000000000000000000000000000..82150ac035079c3b700a07f18c2bf88d98c40f0d
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/plateviewer/WellImages.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright 2009 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.plateviewer;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImage;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImages;
+
+/**
+ * Images of one well.
+ *
+ * @author Tomasz Pylak
+ */
+public class WellImages
+{
+ private String[/* channel */][/* tile number */] imagePaths;
+
+ private final int tileRowsNum;
+
+ private final int tileColsNum;
+
+ private final int channelsNum;
+
+ private final String downloadUrl;
+
+ public WellImages(PlateImageParameters imageParams, String downloadUrl)
+ {
+ int tilesNum = imageParams.getTileRowsNum() * imageParams.getTileColsNum();
+ this.tileRowsNum = imageParams.getTileRowsNum();
+ this.tileColsNum = imageParams.getTileColsNum();
+ this.channelsNum = imageParams.getChannelsNum();
+ this.downloadUrl = downloadUrl;
+ this.imagePaths = new String[imageParams.getChannelsNum()][tilesNum];
+ }
+
+ public WellImages(TileImages images)
+ {
+ this(images.getImageParameters(), images.getDownloadUrl());
+ for (TileImage image : images.getImages())
+ {
+ addImage(image);
+ }
+ }
+
+ public void addImage(TileImage image)
+ {
+ int channelIx = image.getChannel() - 1;
+ int tileIx = image.getTile() - 1;
+ assert imagePaths != null && imagePaths[channelIx][tileIx] == null : "duplicated image for channelIx = "
+ + channelIx + ", tileIx = " + tileIx;
+ imagePaths[channelIx][tileIx] = image.getImagePath();
+ }
+
+ public String tryGetImagePath(int channel, int tile)
+ {
+ return imagePaths[channel - 1][tile - 1];
+ }
+
+ public int getTileRowsNum()
+ {
+ return tileRowsNum;
+ }
+
+ public int getTileColsNum()
+ {
+ return tileColsNum;
+ }
+
+ public int getChannelsNum()
+ {
+ return channelsNum;
+ }
+
+ public String getDownloadUrl()
+ {
+ return downloadUrl;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/utils/GuiUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/utils/GuiUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..3dfd740bd8fc694ddc0475b6447ac87e750c3451
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/utils/GuiUtils.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2009 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.utils;
+
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.Text;
+import com.extjs.gxt.ui.client.widget.layout.TableData;
+import com.extjs.gxt.ui.client.widget.layout.TableLayout;
+import com.google.gwt.user.client.ui.Widget;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class GuiUtils
+{
+ public static void replaceLastItem(LayoutContainer container, Widget newLastWidget)
+ {
+ int lastItemIx = container.getItemCount() - 1;
+ container.remove(container.getWidget(lastItemIx));
+ container.insert(newLastWidget, lastItemIx);
+ container.layout();
+ }
+
+ public static Widget withLabel(Widget component, String label)
+ {
+ return withLabel(component, label, 0);
+ }
+
+ public static Widget withLabel(Widget component, String label, int margin)
+ {
+ LayoutContainer c = new LayoutContainer();
+ c.setLayout(new TableLayout(2));
+ TableData cellLayout = new TableData();
+ cellLayout.setMargin(4);
+ Text labelWidget = new Text(label);
+ labelWidget.setWidth(Math.max(label.length() * 9, 80));
+ c.add(labelWidget, cellLayout);
+ c.add(component);
+ return 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 7de63eda5a50310f347ec14af3a1f06735425742..688a08e08ab1743d94bfa6cc997a5da218992e4f 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
@@ -69,7 +69,7 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
ExperimentIdentifier experimentIdentifier)
{
logTracking(sessionToken, "getPlateLocations",
- "geneMaterialId(%d) experimentIdentifier(%s)", geneMaterialId.getId(),
+ "geneMaterialId(%s) experimentIdentifier(%s)", geneMaterialId.getId(),
experimentIdentifier);
return null;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
index 3d78f4e09ee09e8397f371882f33fccc2a63a49c..621422325fc1663cec566ea1e4a8bd3af24ad241 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
@@ -45,13 +45,13 @@ public interface IScreeningQuery extends BaseQuery
+ " sample_properties well_props, materials well_material, material_properties well_material_props, "
+ " sample_types pl_type, sample_types well_type, material_types well_material_type "
+ "where "
- + "-- find 'well' belonging to the plate which belongs to this experiment "
+ // find 'well' belonging to the plate which belongs to this experiment
+ "exp.id = ?{2} and pl.expe_id = exp.id and well.samp_id_part_of = pl.id and "
- + "-- find 'well_material' assigned to the well "
+ // find 'well_material' assigned to the well
+ "well_props.samp_id = well.id and well_material.id = well_props.mate_prop_id and "
- + "-- well content material property must point to the specified gene id "
+ // well content material property must point to the specified gene id
+ "well_material_props.mate_id = well_material.id and well_material_props.mate_prop_id = ?{1} and "
- + "-- additional joins to entity type tables "
+ // additional joins to entity type tables
+ "pl_type.id = pl.saty_id and well_type.id = well.saty_id and "
+ "well_material_type.id = well_material.maty_id ")
public DataIterator<WellLocation> getPlateLocations(long geneMaterialId, long experimentId);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetLoader.java
new file mode 100644
index 0000000000000000000000000000000000000000..23e6e68c1ce8e4436a6138718fae7a8a9f5b0339
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/DatasetLoader.java
@@ -0,0 +1,122 @@
+/*
+ * Copyright 2009 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.server.logic;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ImageTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImage;
+
+/**
+ * Loads content of datasets by contacting DSS.
+ *
+ * @author Tomasz Pylak
+ */
+public class DatasetLoader
+{
+ public static List<TileImage> loadImages(List<String> datasets, String datastoreCode,
+ IExternalDataTable externalDataTable)
+ {
+ TableModel plateReport =
+ externalDataTable.createReportFromDatasets(
+ ScreeningConstants.PLATE_VIEWER_REPORT_KEY, datastoreCode, datasets);
+ return asImageList(plateReport);
+ }
+
+ public static List<PlateImageParameters> loadImageParameters(List<String> datasets,
+ String datastoreCode, IExternalDataTable externalDataTable)
+ {
+ TableModel imageParamsReport =
+ externalDataTable.createReportFromDatasets(
+ ScreeningConstants.PLATE_IMAGE_PARAMS_REPORT_KEY, datastoreCode, datasets);
+ return asImageParams(imageParamsReport);
+ }
+
+ private static List<PlateImageParameters> asImageParams(TableModel imageParamsReport)
+ {
+ List<PlateImageParameters> paramsList = new ArrayList<PlateImageParameters>();
+ for (TableModelRow tableModelRow : imageParamsReport.getRows())
+ {
+ paramsList.add(asImageParams(tableModelRow));
+ }
+ return paramsList;
+ }
+
+ private static PlateImageParameters asImageParams(TableModelRow tableModelRow)
+ {
+ PlateImageParameters params = new PlateImageParameters();
+ List<ISerializableComparable> values = tableModelRow.getValues();
+ params.setDatasetCode(asText(values.get(0)));
+ params.setRowsNum(asNum(values.get(1)));
+ params.setColsNum(asNum(values.get(2)));
+ params.setTileRowsNum(asNum(values.get(3)));
+ params.setTileColsNum(asNum(values.get(4)));
+ params.setChannelsNum(asNum(values.get(5)));
+ return params;
+ }
+
+ /**
+ * @param plateImages report of a screening plugun with images for the whole plate
+ */
+ private static final List<TileImage> asImageList(TableModel plateReport)
+ {
+ List<TableModelRow> rows = plateReport.getRows();
+ List<TileImage> images = new ArrayList<TileImage>();
+ for (TableModelRow row : rows)
+ {
+ images.add(createImage(row));
+ }
+ return images;
+ }
+
+ // creates a DTO for an image from an unstructured report row
+ private static TileImage createImage(TableModelRow row)
+ {
+ List<ISerializableComparable> values = row.getValues();
+ TileImage image = new TileImage();
+ image.setDatasetCode(asText(values.get(0)));
+ image.setRow(asNum(values.get(1)));
+ image.setColumn(asNum(values.get(2)));
+ image.setTile(asNum(values.get(3)));
+ image.setChannel(asNum(values.get(4)));
+ image.setImagePath(asImagePath(values.get(5)));
+ return image;
+ }
+
+ private static String asText(ISerializableComparable serializableComparable)
+ {
+ return serializableComparable.toString();
+ }
+
+ private static String asImagePath(ISerializableComparable serializableComparable)
+ {
+ return ((ImageTableCell) serializableComparable).getPath();
+ }
+
+ private static int asNum(ISerializableComparable serializableComparable)
+ {
+ return (int) ((IntegerTableCell) serializableComparable).getNumber();
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
index ac33219be8c88b658aa5a000791a176b37d410d4..790c6b4d12e1c669d4bdb69dae787d72b4d6927a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java
@@ -18,22 +18,41 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.sql.Connection;
import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.QueryTool;
+import org.apache.commons.lang.builder.ToStringBuilder;
+
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.common.geometry.ConversionUtils;
+import ch.systemsx.cisd.common.geometry.Point;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.common.utilities.ModifiedShortPrefixToStringStyle;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityReference;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImage;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
/**
@@ -57,16 +76,286 @@ public class GenePlateLocationsLoader
private final IDAOFactory daoFactory;
+ private final IExternalDataTable externalDataTable;
+
private GenePlateLocationsLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
this.daoFactory = daoFactory;
+ this.externalDataTable = businessObjectFactory.createExternalDataTable(session);
+
}
private List<WellLocation> getPlateLocations(TechId geneMaterialId,
ExperimentIdentifier experimentIdentifier)
+ {
+ List<WellLocation> locations = loadLocations(geneMaterialId, experimentIdentifier);
+ List<ExternalDataPE> imageDatasets = loadImageDatasets(locations, externalDataTable);
+ ImagesWithParams images = tryLoadImagesReport(imageDatasets);
+ if (images != null)
+ {
+ enrichWithImages(locations, imageDatasets, images);
+ }
+ return locations;
+ }
+
+ private static void enrichWithImages(List<WellLocation> locations,
+ List<ExternalDataPE> imageDatasets, ImagesWithParams images)
+ {
+ Map<WellPointer, List<TileImage>> imageMap = asMap(images.getImages());
+ Map<Long/* plate id */, String/* datasetCode */> plateToDatasetMap =
+ createPlateToDatasetMap(imageDatasets);
+ Map<String, ExternalDataPE> datasetMap = asSampleMap(imageDatasets);
+
+ for (WellLocation loc : locations)
+ {
+ WellPointer pointer = tryCreateWellPointer(plateToDatasetMap, loc);
+ if (pointer != null)
+ {
+ List<TileImage> tiles = imageMap.get(pointer);
+ if (tiles != null)
+ {
+ ExternalDataPE dataset = datasetMap.get(pointer.getDatasetCode());
+ PlateImageParameters imageParameters =
+ images.getParamsMap().get(dataset.getCode());
+ TileImages wellImages =
+ TileImages.create(createReference(dataset), tiles, imageParameters);
+ loc.setImages(wellImages);
+ }
+ }
+ }
+ }
+
+ private static DatasetReference createReference(ExternalDataPE dataset)
+ {
+ DataStorePE dataStore = dataset.getDataStore();
+ return new DatasetReference(dataset.getCode(), dataStore.getCode(), dataStore
+ .getDownloadUrl());
+ }
+
+ private static WellPointer tryCreateWellPointer(Map<Long, String> plateToDatasetMap,
+ WellLocation location)
+ {
+ String datasetCode = plateToDatasetMap.get(location.getPlate().getId());
+ if (datasetCode != null)
+ {
+ EntityReference well = location.getWell();
+ String wellCode = well.getCode();
+ Point wellLoc = ConversionUtils.parseSpreadsheetLocation(wellCode);
+ return new WellPointer(datasetCode, wellLoc.getX() + 1, wellLoc.getY() + 1);
+ } else
+ {
+ return null;
+ }
+ }
+
+ private static Map<Long, String> createPlateToDatasetMap(List<ExternalDataPE> datasets)
+ {
+ Map<Long, String> map = new HashMap<Long, String>();
+ for (ExternalDataPE dataset : datasets)
+ {
+ map.put(dataset.tryGetSample().getId(), dataset.getCode());
+ }
+ return map;
+ }
+
+ private static Map<WellPointer, List<TileImage>> asMap(List<TileImage> images)
+ {
+ Map<WellPointer, List<TileImage>> map = new HashMap<WellPointer, List<TileImage>>();
+ for (TileImage image : images)
+ {
+ WellPointer pointer = WellPointer.create(image);
+ List<TileImage> list = map.get(pointer);
+ if (list == null)
+ {
+ list = new ArrayList<TileImage>();
+ map.put(pointer, list);
+ }
+ list.add(image);
+ }
+ return map;
+ }
+
+ private static class WellPointer
+ {
+ private static WellPointer create(TileImage image)
+ {
+ return new WellPointer(image.getDatasetCode(), image.getRow(), image.getColumn());
+ }
+
+ private final String datasetCode;
+
+ private final int row;
+
+ private final int column;
+
+ public WellPointer(String datasetCode, int row, int column)
+ {
+ this.datasetCode = datasetCode;
+ this.row = row;
+ this.column = column;
+ }
+
+ public String getDatasetCode()
+ {
+ return datasetCode;
+ }
+
+ public int getRow()
+ {
+ return row;
+ }
+
+ public int getColumn()
+ {
+ return column;
+ }
+
+ @Override
+ public final boolean equals(final Object obj)
+ {
+ WellPointer that = (WellPointer) obj;
+ return row == that.row && column == that.column && datasetCode.equals(that.datasetCode);
+ }
+
+ @Override
+ public final int hashCode()
+ {
+ return (column * 2343 + row * 9876) ^ datasetCode.hashCode();
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this,
+ ModifiedShortPrefixToStringStyle.MODIFIED_SHORT_PREFIX_STYLE);
+ }
+ }
+
+ private ImagesWithParams tryLoadImagesReport(List<ExternalDataPE> imageDatasets)
+ {
+ if (imageDatasets.size() == 0)
+ {
+ return null;
+ }
+ List<String> datasetCodes = asCodes(imageDatasets);
+ // NOTE: assumes that all datasets are from the same datastore
+ String datastoreCode = imageDatasets.get(0).getDataStore().getCode();
+ List<TileImage> images =
+ DatasetLoader.loadImages(datasetCodes, datastoreCode, externalDataTable);
+ List<PlateImageParameters> imageParameters =
+ DatasetLoader.loadImageParameters(datasetCodes, datastoreCode, externalDataTable);
+ return new ImagesWithParams(images, imageParameters);
+ }
+
+ private static class ImagesWithParams extends AbstractHashable
+ {
+ private List<TileImage> images;
+
+ private Map<String/* dataset code */, PlateImageParameters> paramsMap;
+
+ public ImagesWithParams(List<TileImage> images, List<PlateImageParameters> imageParameters)
+ {
+ this.images = images;
+ this.paramsMap = asMap(imageParameters);
+ }
+
+ private static Map<String, PlateImageParameters> asMap(
+ List<PlateImageParameters> imageParameters)
+ {
+ Map<String, PlateImageParameters> map = new HashMap<String, PlateImageParameters>();
+ for (PlateImageParameters params : imageParameters)
+ {
+ map.put(params.getDatasetCode(), params);
+ }
+ return map;
+ }
+
+ public List<TileImage> getImages()
+ {
+ return images;
+ }
+
+ public Map<String, PlateImageParameters> getParamsMap()
+ {
+ return paramsMap;
+ }
+ }
+
+ private static List<String> asCodes(List<ExternalDataPE> datasets)
+ {
+ List<String> codes = new ArrayList<String>();
+ for (ExternalDataPE dataset : datasets)
+ {
+ codes.add(dataset.getCode());
+ }
+ return codes;
+ }
+
+ private static Map<String/* dataset code */, ExternalDataPE> asSampleMap(
+ List<ExternalDataPE> datasets)
+ {
+ Map<String, ExternalDataPE> map = new HashMap<String, ExternalDataPE>();
+ for (ExternalDataPE dataset : datasets)
+ {
+ map.put(dataset.getCode(), dataset);
+ }
+ return map;
+ }
+
+ private static List<ExternalDataPE> loadImageDatasets(List<WellLocation> locations,
+ IExternalDataTable externalDataTable)
+ {
+ List<ExternalDataPE> imageDatasets = new ArrayList<ExternalDataPE>();
+ List<TechId> plateIds = extractPlateIds(locations);
+ for (TechId plateId : plateIds)
+ {
+ List<ExternalDataPE> datasets =
+ PlateContentLoader.loadDatasets(plateId, externalDataTable);
+ imageDatasets.addAll(filterImageDatasets(datasets));
+ }
+ return imageDatasets;
+ }
+
+ private static List<ExternalDataPE> filterImageDatasets(List<ExternalDataPE> datasets)
+ {
+ List<ExternalDataPE> result = new ArrayList<ExternalDataPE>();
+ for (ExternalDataPE dataset : datasets)
+ {
+ if (dataset.getDataSetType().getCode().equalsIgnoreCase(
+ ScreeningConstants.IMAGE_DATASET_TYPE))
+ {
+ result.add(dataset);
+ }
+ }
+ return result;
+ }
+
+ private static List<TechId> extractPlateIds(List<WellLocation> locations)
+ {
+ Set<Long> ids = new HashSet<Long>();
+ for (WellLocation loc : locations)
+ {
+ ids.add(loc.getPlate().getId());
+ }
+ return asTechIdList(ids);
+ }
+
+ private static List<TechId> asTechIdList(Set<Long> ids)
+ {
+ List<TechId> result = new ArrayList<TechId>();
+ Iterator<Long> iter = ids.iterator();
+ while (iter.hasNext())
+ {
+ result.add(new TechId(iter.next()));
+ }
+ return result;
+ }
+
+ private List<WellLocation> loadLocations(TechId geneMaterialId,
+ ExperimentIdentifier experimentIdentifier)
{
long experimentId = loadExperimentId(experimentIdentifier);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index e93c746891976ad37fd836e09d0eaf5ba3532875..317a359bc211df6240e9052b42b84adef8bf2f8a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -30,7 +30,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -40,8 +39,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.ScreeningCons
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImage;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImage;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
@@ -76,7 +76,7 @@ public class PlateContentLoader
Sample plate = loadPlate(plateId);
List<ExternalDataPE> datasets = loadDatasets(plateId, externalDataTable);
- PlateImages images = tryLoadImages(datasets, externalDataTable);
+ TileImages images = tryLoadImages(datasets, externalDataTable);
List<WellMetadata> wells = loadWells(plateId);
DatasetReference imageAnalysisDataset = tryFindImageAnalysisDataset(datasets);
@@ -97,7 +97,9 @@ public class PlateContentLoader
tryFindDataset(datasets, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
if (dataset != null)
{
- return new DatasetReference(dataset.getCode(), dataset.getDataStore().getCode());
+ DataStorePE dataStore = dataset.getDataStore();
+ return new DatasetReference(dataset.getCode(), dataStore.getCode(), dataStore
+ .getDownloadUrl());
} else
{
return null;
@@ -119,7 +121,7 @@ public class PlateContentLoader
return createWells(wells);
}
- private PlateImages tryLoadImages(List<ExternalDataPE> datasets,
+ private TileImages tryLoadImages(List<ExternalDataPE> datasets,
IExternalDataTable externalDataTable)
{
ExternalDataPE dataset = tryFindDataset(datasets, ScreeningConstants.IMAGE_DATASET_TYPE);
@@ -132,28 +134,27 @@ public class PlateContentLoader
}
}
- private List<ExternalDataPE> loadDatasets(TechId plateId, IExternalDataTable externalDataTable)
+ protected static List<ExternalDataPE> loadDatasets(TechId plateId,
+ IExternalDataTable externalDataTable)
{
externalDataTable.loadBySampleTechId(plateId);
List<ExternalDataPE> externalData = externalDataTable.getExternalData();
return externalData;
}
- private PlateImages loadImages(IExternalDataTable externalDataTable, ExternalDataPE dataset)
+ private TileImages loadImages(IExternalDataTable externalDataTable, ExternalDataPE dataset)
{
DataStorePE dataStore = dataset.getDataStore();
String datasetCode = dataset.getCode();
List<String> datasets = Arrays.asList(datasetCode);
String datastoreCode = dataStore.getCode();
- TableModel plateReport =
- externalDataTable.createReportFromDatasets(
- ScreeningConstants.PLATE_VIEWER_REPORT_KEY, datastoreCode, datasets);
- TableModel imageParamsReport =
- externalDataTable.createReportFromDatasets(
- ScreeningConstants.PLATE_IMAGE_PARAMS_REPORT_KEY, datastoreCode, datasets);
+ List<TileImage> plateReport =
+ DatasetLoader.loadImages(datasets, datastoreCode, externalDataTable);
+ List<PlateImageParameters> imageParamsReports =
+ DatasetLoader.loadImageParameters(datasets, datastoreCode, externalDataTable);
- return PlateImage.createImages(new DatasetReference(datasetCode, datastoreCode), dataStore
- .getDownloadUrl(), plateReport, imageParamsReport);
+ return TileImages.create(new DatasetReference(datasetCode, datastoreCode, dataStore
+ .getDownloadUrl()), plateReport, imageParamsReports.get(0));
}
private static ExternalDataPE tryFindDataset(List<ExternalDataPE> datasets, String datasetType)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/DatasetReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/DatasetReference.java
index 523b8d43e3434d9f67612470cac6bf19c65ff718..f6baa9626337a4750aacae34e0370936e7654d94 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/DatasetReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/DatasetReference.java
@@ -25,25 +25,28 @@ import com.google.gwt.user.client.rpc.IsSerializable;
*/
public class DatasetReference implements IsSerializable
{
- private String code;
+ private String datasetCode;
private String datastoreCode;
+ private String downloadUrl;
+
// GWT only
@SuppressWarnings("unused")
private DatasetReference()
{
}
- public DatasetReference(String code, String datastoreCode)
+ public DatasetReference(String code, String datastoreCode, String downloadUrl)
{
- this.code = code;
+ this.datasetCode = code;
this.datastoreCode = datastoreCode;
+ this.downloadUrl = downloadUrl;
}
public String getCode()
{
- return code;
+ return datasetCode;
}
public String getDatastoreCode()
@@ -51,4 +54,9 @@ public class DatasetReference implements IsSerializable
return datastoreCode;
}
+ public String getDownloadUrl()
+ {
+ return downloadUrl;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java
index 2023c683801aea066029dbcf2b6ed822b457ffbb..20c26536220904dfd363e80cef22af3d969f4c3b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java
@@ -33,7 +33,7 @@ public class PlateContent implements IsSerializable
private List<WellMetadata> wells;
- private PlateImages imagesOrNull;
+ private TileImages imagesOrNull;
private DatasetReference imageAnalysisDatasetOrNull;
@@ -43,7 +43,7 @@ public class PlateContent implements IsSerializable
{
}
- public PlateContent(Sample plate, List<WellMetadata> wells, PlateImages imagesOrNull,
+ public PlateContent(Sample plate, List<WellMetadata> wells, TileImages imagesOrNull,
DatasetReference imageAnalysisDatasetOrNull)
{
this.plate = plate;
@@ -58,7 +58,7 @@ public class PlateContent implements IsSerializable
}
/** can be null */
- public PlateImages tryGetImages()
+ public TileImages tryGetImages()
{
return imagesOrNull;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImage.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImage.java
deleted file mode 100644
index 8726cb8691fa26fe12080759b238bdc706f06a80..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImage.java
+++ /dev/null
@@ -1,172 +0,0 @@
-/*
- * Copyright 2009 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.google.gwt.user.client.rpc.IsSerializable;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ImageTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
-
-/**
- * @author Tomasz Pylak
- */
-public class PlateImage implements IsSerializable
-{
- // -------- column headers used in a DSS service to describe images for a plate ------
-
- public static final String IMAGE = "Thumbnail";
-
- public static final String CHANNEL = "Channel";
-
- public static final String TILE = "Tile";
-
- public static final String COLUMN = "Column";
-
- public static final String ROW = "Row";
-
- public static final String DATASET_CODE = "Dataset Code";
-
- // ----------
-
- /**
- * @param plateReport report of a screening plugun with images for the whole plate
- */
- public static final PlateImages createImages(DatasetReference dataset, String downloadUrl,
- TableModel plateReport, TableModel imageParamsReport)
- {
- return new PlateImages(dataset, downloadUrl, createImageList(plateReport),
- createImageParams(imageParamsReport));
- }
-
- private static PlateImageParameters createImageParams(TableModel imageParamsReport)
- {
- PlateImageParameters params = new PlateImageParameters();
- assert imageParamsReport.getRows().size() == 1 : "exactly one row expected in imageParamsReport";
- List<ISerializableComparable> values = imageParamsReport.getRows().get(0).getValues();
-
- params.setRowsNum(asNum(values.get(0)));
- params.setColsNum(asNum(values.get(1)));
- params.setTileRowsNum(asNum(values.get(2)));
- params.setTileColsNum(asNum(values.get(3)));
- params.setChannelsNum(asNum(values.get(4)));
- return params;
- }
-
- private static final List<PlateImage> createImageList(TableModel plateReport)
- {
- List<TableModelRow> rows = plateReport.getRows();
- List<PlateImage> images = new ArrayList<PlateImage>();
- for (TableModelRow row : rows)
- {
- images.add(createImage(row));
- }
- return images;
- }
-
- // creates a DTO for an image from an unstructured report row
- private static PlateImage createImage(TableModelRow row)
- {
- List<ISerializableComparable> values = row.getValues();
- PlateImage image = new PlateImage();
- image.setRow(asNum(values.get(1)));
- image.setColumn(asNum(values.get(2)));
- image.setTile(asNum(values.get(3)));
- image.setChannel(asNum(values.get(4)));
- image.setImagePath(asImagePath(values.get(5)));
- return image;
- }
-
- private static String asImagePath(ISerializableComparable serializableComparable)
- {
- return ((ImageTableCell) serializableComparable).getPath();
- }
-
- private static int asNum(ISerializableComparable serializableComparable)
- {
- return (int) ((IntegerTableCell) serializableComparable).getNumber();
- }
-
- // ------------------------------------------
-
- private String imagePath;
-
- private int row;
-
- private int column;
-
- private int tile;
-
- private int channel;
-
- public String getImagePath()
- {
- return imagePath;
- }
-
- public void setImagePath(String imagePath)
- {
- this.imagePath = imagePath;
- }
-
- 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;
- }
-
- /** numbered from 1 */
- public int getTile()
- {
- return tile;
- }
-
- public void setTile(int tile)
- {
- this.tile = tile;
- }
-
- /** numbered from 1 */
- public int getChannel()
- {
- return channel;
- }
-
- public void setChannel(int channel)
- {
- this.channel = channel;
- }
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java
index 376532763ddfc4a06e4ca11982ee72ac95ee50f7..9e2c6adda15b539b3f7a071bd79b64c745ff5779 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java
@@ -25,19 +25,8 @@ import com.google.gwt.user.client.rpc.IsSerializable;
*/
public class PlateImageParameters implements IsSerializable
{
- // -------- column headers used in a DSS service to describe images for a plate ------
-
- public static final String ROWS = "Rows";
-
- public static final String COLUMNS = "Columns";
-
- public static final String TILE_ROWS_NUM = "Tile rows";
-
- public static final String TILE_COLS_NUM = "Tile columns";
-
- public static final String CHANNELS_NUM = "Number of channels";
-
- // ----------
+ // dataset code for which plate parameters are valid
+ private String datasetCode;
private int rowsNum;
@@ -99,4 +88,13 @@ public class PlateImageParameters implements IsSerializable
this.channelsNum = channelsNum;
}
+ public String getDatasetCode()
+ {
+ return datasetCode;
+ }
+
+ public void setDatasetCode(String datasetCode)
+ {
+ this.datasetCode = datasetCode;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/TileImage.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/TileImage.java
new file mode 100644
index 0000000000000000000000000000000000000000..d4b4f91da53c0deae716e41c24e2a7111854954b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/TileImage.java
@@ -0,0 +1,101 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+/**
+ * Image of one tile in one channel.
+ *
+ * @author Tomasz Pylak
+ */
+public class TileImage implements IsSerializable
+{
+ private String datasetCode;
+
+ private String imagePath;
+
+ private int row;
+
+ private int column;
+
+ private int tile;
+
+ private int channel;
+
+ public String getImagePath()
+ {
+ return imagePath;
+ }
+
+ public void setImagePath(String imagePath)
+ {
+ this.imagePath = imagePath;
+ }
+
+ 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;
+ }
+
+ /** numbered from 1 */
+ public int getTile()
+ {
+ return tile;
+ }
+
+ public void setTile(int tile)
+ {
+ this.tile = tile;
+ }
+
+ /** numbered from 1 */
+ public int getChannel()
+ {
+ return channel;
+ }
+
+ public void setChannel(int channel)
+ {
+ this.channel = channel;
+ }
+
+ public String getDatasetCode()
+ {
+ return datasetCode;
+ }
+
+ public void setDatasetCode(String datasetCode)
+ {
+ this.datasetCode = datasetCode;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/TileImages.java
similarity index 70%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/TileImages.java
index a035a73d555b8dff28d78ae10eb3397ef8f5b41e..cbdbc436cc804e1cae0ba6d68305c34f9f1fecb4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/TileImages.java
@@ -21,38 +21,41 @@ import java.util.List;
import com.google.gwt.user.client.rpc.IsSerializable;
/**
- * Describes images in one dataset and the way to fetch them.
+ * Describes images in one dataset and URLs to them.
*
* @author Tomasz Pylak
*/
-public class PlateImages implements IsSerializable
+public class TileImages implements IsSerializable
{
- private DatasetReference dataset;
+ public static final TileImages create(DatasetReference dataset, List<TileImage> plateImages,
+ PlateImageParameters imageParams)
+ {
+ return new TileImages(dataset, plateImages, imageParams);
+ }
- private String downloadUrl;
+ private DatasetReference dataset;
- private List<PlateImage> images;
+ private List<TileImage> images;
private PlateImageParameters imageParameters;
// GWT only
@SuppressWarnings("unused")
- private PlateImages()
+ private TileImages()
{
}
- public PlateImages(DatasetReference dataset, String downloadUrl,
- List<PlateImage> images, PlateImageParameters imageParameters)
+ public TileImages(DatasetReference dataset, List<TileImage> images,
+ PlateImageParameters imageParameters)
{
this.dataset = dataset;
- this.downloadUrl = downloadUrl;
this.images = images;
this.imageParameters = imageParameters;
}
public String getDownloadUrl()
{
- return downloadUrl;
+ return dataset.getDownloadUrl();
}
public String getDatasetCode()
@@ -65,7 +68,7 @@ public class PlateImages implements IsSerializable
return dataset.getDatastoreCode();
}
- public List<PlateImage> getImages()
+ public List<TileImage> getImages()
{
return images;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellLocation.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellLocation.java
index 80adfdb79a6e5831c270bda637619361deb9a9d7..14392a8258ddc8aebf118d2aa76b9a0e74846717 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellLocation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellLocation.java
@@ -31,6 +31,9 @@ public class WellLocation implements IsSerializable
private EntityReference materialContent;
+ // contains only images for this well
+ private TileImages imagesOrNull;
+
// GWT only
@SuppressWarnings("unused")
private WellLocation()
@@ -58,4 +61,14 @@ public class WellLocation implements IsSerializable
{
return materialContent;
}
+
+ public TileImages tryGetImages()
+ {
+ return imagesOrNull;
+ }
+
+ public void setImages(TileImages images)
+ {
+ this.imagesOrNull = images;
+ }
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/.gitignore b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/.gitignore
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ServerInterfaceRegressionTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ServerInterfaceRegressionTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..1a41070434f1e68617a9f89a7cc2fc50e2306fe6
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ServerInterfaceRegressionTest.java
@@ -0,0 +1,33 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.shared;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.RegressionTestCase;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ServerInterfaceRegressionTest extends RegressionTestCase
+{
+ @Test
+ public void testServerAnnotations()
+ {
+ assertMandatoryMethodAnnotations(IScreeningServer.class);
+ }
+}