From e0fc264e44ce6cc50d75c2037123dc88e70e17e6 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 10 Feb 2010 08:40:01 +0000
Subject: [PATCH] LMS-1338 Show plate visualisation in dataset view
SVN: 14673
---
.../web/client/IScreeningClientService.java | 7 +
.../client/IScreeningClientServiceAsync.java | 5 +
.../detailviewers/PlateDatasetViewer.java | 3 +-
.../PlateLayoutDatasetSection.java | 89 ++++++
.../PlateLayoutSampleSection.java | 179 +++++++++++
...eLayoutSection.java => PlateLayouter.java} | 296 ++++++------------
.../detailviewers/PlateSampleViewer.java | 2 +-
.../application/detailviewers/WellData.java | 16 +-
.../web/server/PlateMetadataProvider.java | 29 +-
.../web/server/ScreeningClientService.java | 12 +
.../IScreeningBusinessObjectFactory.java | 3 +
.../ScreeningBusinessObjectFactory.java | 6 +
.../screening/server/ScreeningServer.java | 7 +
.../server/ScreeningServerLogger.java | 18 +-
.../server/logic/PlateContentLoader.java | 52 ++-
.../screening/shared/IScreeningServer.java | 14 +-
.../shared/basic/dto/PlateContent.java | 57 +---
.../shared/basic/dto/PlateImages.java | 92 ++++++
18 files changed, 600 insertions(+), 287 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutDatasetSection.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSampleSection.java
rename screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/{PlateLayoutSection.java => PlateLayouter.java} (57%)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
index c9ce265d97d..5cdfd90f7b9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
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.WellContent;
/**
@@ -67,6 +68,12 @@ public interface IScreeningClientService extends IClientService
*/
public PlateContent getPlateContent(TechId sampleId) throws UserFailureException;
+ /**
+ * Fetches information about a plate: metadata and images for wells. The specified dataset is
+ * supposed to be in BDS-HCS format.
+ */
+ public PlateImages getPlateContentForDataset(TechId datasetId);
+
/**
* @return well locations which belong to a parent plate connected to a specified experiment.
* Each well will have a material property (e.g. oligo), which is connected through
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
index 0b305f9ddad..666829ac2fe 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
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.WellContent;
/**
@@ -51,6 +52,10 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
/** @see IScreeningClientService#getPlateContent(TechId) */
public void getPlateContent(TechId sampleId, final AsyncCallback<PlateContent> callback);
+ /** @see IScreeningClientService#getPlateContentForDataset(TechId) */
+ public void getPlateContentForDataset(TechId datasetId,
+ AsyncCallback<PlateImages> createDisplayPlateCallback);
+
/** @see IScreeningClientService#getDataSetInfo(TechId) */
public void getDataSetInfo(TechId datasetTechId, AsyncCallback<ExternalData> callback);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateDatasetViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateDatasetViewer.java
index be432586753..aec6262d48e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateDatasetViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateDatasetViewer.java
@@ -63,8 +63,7 @@ public final class PlateDatasetViewer extends GenericDataSetViewer
protected List<SingleSectionPanel> createAdditionalSectionPanels()
{
List<SingleSectionPanel> sections = new ArrayList<SingleSectionPanel>();
- // TODO 2010-02-09, Tomasz Pylak: implement me
- // sections.add(PlateLayoutSection.createForDataset(screeningViewContext, datasetId));
+ sections.add(new PlateLayoutDatasetSection(screeningViewContext, datasetId));
return sections;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutDatasetSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutDatasetSection.java
new file mode 100644
index 00000000000..ed79a7d18bf
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutDatasetSection.java
@@ -0,0 +1,89 @@
+/*
+ * 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.detailviewers;
+
+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.button.Button;
+import com.extjs.gxt.ui.client.widget.layout.RowLayout;
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
+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.SingleSectionPanel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
+
+/**
+ * A section of dataset detail view for datasets containing HCS images. Shows where the oligo and
+ * gene samples are located on the plate and allow to check the content of the well quickly.
+ *
+ * @author Tomasz Pylak
+ */
+public class PlateLayoutDatasetSection extends SingleSectionPanel
+{
+ public static final String ID_SUFFIX = "PlateLayoutDatasetSection";
+
+ public PlateLayoutDatasetSection(ScreeningViewContext viewContext, TechId datasetId)
+ {
+ super("Plate Layout");
+ add(new Text(viewContext.getMessage(Dict.LOAD_IN_PROGRESS)));
+ viewContext.getService().getPlateContentForDataset(datasetId,
+ createDisplayPlateCallback(viewContext));
+ setDisplayID(DisplayTypeIDGenerator.SAMPLE_SECTION, ID_SUFFIX);
+ }
+
+ private AsyncCallback<PlateImages> createDisplayPlateCallback(final ScreeningViewContext context)
+ {
+ return new AbstractAsyncCallback<PlateImages>(context)
+ {
+ @Override
+ protected void process(PlateImages plateContent)
+ {
+ removeAll();
+ setLayout(new RowLayout());
+ setScrollMode(Scroll.AUTO);
+
+ renderPlate(plateContent, context);
+ addMetadataTable(plateContent.getPlate(), context);
+
+ layout();
+ }
+ };
+ }
+
+ private void renderPlate(PlateImages plateImages, ScreeningViewContext viewContext)
+ {
+ LayoutContainer container = new LayoutContainer();
+ container.add(PlateLayouter.createVisualization(plateImages, viewContext));
+ add(container, PlateLayouter.createRowLayoutMarginData());
+ }
+
+ private void addMetadataTable(final Sample plate,
+ final IViewContext<IScreeningClientServiceAsync> viewContext)
+ {
+ Button generateButton = PlateLayouter.createPlateMetadataButton(plate, viewContext);
+ add(generateButton, PlateLayouter.createRowLayoutMarginData());
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSampleSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSampleSection.java
new file mode 100644
index 00000000000..681f9ee46c0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSampleSection.java
@@ -0,0 +1,179 @@
+/*
+ * 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.detailviewers;
+
+import java.util.Arrays;
+
+import com.extjs.gxt.ui.client.Style.Scroll;
+import com.extjs.gxt.ui.client.event.ButtonEvent;
+import com.extjs.gxt.ui.client.event.SelectionListener;
+import com.extjs.gxt.ui.client.widget.Component;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.Text;
+import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.layout.RowLayout;
+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.SingleSectionPanel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.data.DataSetReportGenerator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DisplayedOrSelectedDatasetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
+
+/**
+ * A section of plate detail view which shows where the oligo and gene samples are located on the
+ * plate and allow to check the content of the well quickly.
+ *
+ * @author Tomasz Pylak
+ */
+public class PlateLayoutSampleSection extends SingleSectionPanel
+{
+ public static final String ID_SUFFIX = "PlateLayoutSection";
+
+ public PlateLayoutSampleSection(ScreeningViewContext viewContext, TechId sampleId)
+ {
+ super("Plate Layout");
+ add(new Text(viewContext.getMessage(Dict.LOAD_IN_PROGRESS)));
+ viewContext.getService().getPlateContent(sampleId, createDisplayPlateCallback(viewContext));
+ setDisplayID(DisplayTypeIDGenerator.SAMPLE_SECTION, ID_SUFFIX);
+ }
+
+ private AsyncCallback<PlateContent> createDisplayPlateCallback(
+ final ScreeningViewContext context)
+ {
+ return new AbstractAsyncCallback<PlateContent>(context)
+ {
+ @Override
+ protected void process(PlateContent plateContent)
+ {
+ removeAll();
+ setLayout(new RowLayout());
+ setScrollMode(Scroll.AUTO);
+
+ renderPlate(plateContent, context);
+ addImageAnalysisButton(plateContent, viewContext);
+
+ addMetadataTable(plateContent, context);
+
+ layout();
+ }
+ };
+ }
+
+ private void addImageAnalysisButton(final PlateContent plateContent,
+ final IViewContext<?> viewContext)
+ {
+ Component analysisPanel;
+ int datasetsNumber = plateContent.getImageAnalysisDatasetsNumber();
+ final DatasetReference dataset = plateContent.tryGetImageAnalysisDataset();
+ if (dataset != null)
+ {
+ assert datasetsNumber == 1 : "only one image analysis dataset expected, but found: "
+ + datasetsNumber;
+ Button generateButton =
+ new Button("Show Image Analysis Results", new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ generateImageAnalysisReport(viewContext, dataset, plateContent);
+ }
+ });
+ analysisPanel = generateButton;
+ } else
+ {
+ if (datasetsNumber == 0)
+ {
+ analysisPanel = new Text("No image analysis data is available.");
+ } else
+ {
+ analysisPanel =
+ new Text("There are " + datasetsNumber + " analysis datasets, "
+ + "select the one of your interest from the 'Data Sets' section "
+ + "and go to its detail view to see the image analysis results.");
+ }
+ }
+ add(analysisPanel, PlateLayouter.createRowLayoutMarginData());
+ }
+
+ private void generateImageAnalysisReport(IViewContext<?> viewContext, DatasetReference dataset,
+ PlateContent plateContent)
+ {
+ DatastoreServiceDescription service = createImageAnalysisReporter(dataset, plateContent);
+ DisplayedOrSelectedDatasetCriteria criteria =
+ DisplayedOrSelectedDatasetCriteria.createSelectedItems(Arrays.asList(dataset
+ .getCode()));
+ DataSetReportGenerator.generate(viewContext.getCommonViewContext(), service, criteria);
+ }
+
+ private DatastoreServiceDescription createImageAnalysisReporter(DatasetReference dataset,
+ PlateContent plateContent)
+ {
+ String reportLabel = "Image Analysis of " + plateContent.getPlate().getCode();
+ return new DatastoreServiceDescription(ScreeningConstants.PLATE_IMAGE_ANALYSIS_REPORT_KEY,
+ reportLabel, new String[] {}, dataset.getDatastoreCode());
+ }
+
+ private void renderPlate(PlateContent plateContent, ScreeningViewContext viewContext)
+ {
+ LayoutContainer container = new LayoutContainer();
+ Widget datasetNumberLegend = tryRenderImageDatasetsNumberLegend(plateContent, viewContext);
+ if (datasetNumberLegend != null)
+ {
+ container.add(datasetNumberLegend);
+ }
+ container.add(PlateLayouter.createVisualization(plateContent.getPlateImages(), viewContext));
+
+ add(container, PlateLayouter.createRowLayoutMarginData());
+ }
+
+ private Widget tryRenderImageDatasetsNumberLegend(PlateContent plateContent,
+ IViewContext<?> viewContext)
+ {
+ int datasetsNumber = plateContent.getImageDatasetsNumber();
+ if (datasetsNumber == 0)
+ {
+ return new Text("No images data is available.");
+ } else if (datasetsNumber == 1)
+ {
+ return null;
+ } else
+ {
+ return new Text("There are " + datasetsNumber + " datasets with images, "
+ + "select the one of your interest from the 'Data Sets' section "
+ + "and go to its detail view to browse acquired images.");
+ }
+ }
+
+ private void addMetadataTable(final PlateContent plateContent,
+ final IViewContext<IScreeningClientServiceAsync> viewContext)
+ {
+ Button generateButton =
+ PlateLayouter.createPlateMetadataButton(plateContent.getPlate(), viewContext);
+ add(generateButton, PlateLayouter.createRowLayoutMarginData());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayouter.java
similarity index 57%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSection.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayouter.java
index daf0eb615d9..3ef47c606c7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayoutSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateLayouter.java
@@ -1,5 +1,5 @@
/*
- * Copyright 2009 ETH Zuerich, CISD
+ * 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.
@@ -17,10 +17,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
-import com.extjs.gxt.ui.client.Style.Scroll;
import com.extjs.gxt.ui.client.event.BaseEvent;
import com.extjs.gxt.ui.client.event.ButtonEvent;
import com.extjs.gxt.ui.client.event.Events;
@@ -35,204 +33,50 @@ import com.extjs.gxt.ui.client.widget.layout.RowData;
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.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.SingleSectionPanel;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DefaultTabItem;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DispatcherHelper;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DisplayTypeIDGenerator;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItemFactory;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier.HelpPageAction;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier.HelpPageDomain;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.data.DataSetReportGenerator;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.GWTUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DisplayedOrSelectedDatasetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
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.plugin.screening.client.web.client.IScreeningClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.ScreeningConstants;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ChannelChooser.DefaultChannelState;
-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.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
- * A section of plate detail view which shows where the oligo and gene samples are located on the
- * plate and allow to check the content of the well quickly.
+ * Utilities to create plate visualization.
*
* @author Tomasz Pylak
*/
-public class PlateLayoutSection extends SingleSectionPanel
+public class PlateLayouter
{
private static final String CONTROL_MATERIAL_TYPE = "CONTROL";
- public static final String ID_SUFFIX = "PlateLayoutSection";
-
- private final TechId sampleId;
-
- public PlateLayoutSection(ScreeningViewContext viewContext, TechId sampleId)
- {
- super("Plate Layout");
- this.sampleId = sampleId;
- add(new Text(viewContext.getMessage(Dict.LOAD_IN_PROGRESS)));
- viewContext.getService().getPlateContent(sampleId, createDisplayPlateCallback(viewContext));
- setDisplayID(DisplayTypeIDGenerator.SAMPLE_SECTION, ID_SUFFIX);
- }
-
- private AsyncCallback<PlateContent> createDisplayPlateCallback(
- final ScreeningViewContext context)
- {
- return new AbstractAsyncCallback<PlateContent>(context)
- {
- @Override
- protected void process(PlateContent plateContent)
- {
- removeAll();
- setLayout(new RowLayout());
- setScrollMode(Scroll.AUTO);
-
- renderPlate(plateContent, context);
- addImageAnalysisButton(plateContent, viewContext);
-
- addMetadataTable(plateContent, context);
-
- layout();
- }
- };
- }
-
- private void addImageAnalysisButton(final PlateContent plateContent,
- final IViewContext<?> viewContext)
- {
- Component analysisPanel;
- int datasetsNumber = plateContent.getImageAnalysisDatasetsNumber();
- final DatasetReference dataset = plateContent.tryGetImageAnalysisDataset();
- if (dataset != null)
- {
- assert datasetsNumber == 1 : "only one image analysis dataset expected, but found: "
- + datasetsNumber;
- Button generateButton =
- new Button("Show Image Analysis Results", new SelectionListener<ButtonEvent>()
- {
- @Override
- public void componentSelected(ButtonEvent ce)
- {
- generateImageAnalysisReport(viewContext, dataset, plateContent);
- }
- });
- analysisPanel = generateButton;
- } else
- {
- if (datasetsNumber == 0)
- {
- analysisPanel = new Text("No image analysis data is available.");
- } else
- {
- analysisPanel =
- new Text("There are " + datasetsNumber + " analysis datasets, "
- + "select the one of your interest from the 'Data Sets' section "
- + "and go to its detail view to see the image analysis results.");
- }
- }
- add(analysisPanel, createMarginLayoutData());
- }
-
- private void generateImageAnalysisReport(IViewContext<?> viewContext, DatasetReference dataset,
- PlateContent plateContent)
- {
- DatastoreServiceDescription service = createImageAnalysisReporter(dataset, plateContent);
- DisplayedOrSelectedDatasetCriteria criteria =
- DisplayedOrSelectedDatasetCriteria.createSelectedItems(Arrays.asList(dataset
- .getCode()));
- DataSetReportGenerator.generate(viewContext.getCommonViewContext(), service, criteria);
- }
-
- private DatastoreServiceDescription createImageAnalysisReporter(DatasetReference dataset,
- PlateContent plateContent)
- {
- String reportLabel = "Image Analysis of " + plateContent.getPlate().getCode();
- return new DatastoreServiceDescription(ScreeningConstants.PLATE_IMAGE_ANALYSIS_REPORT_KEY,
- reportLabel, new String[] {}, dataset.getDatastoreCode());
- }
-
- private void renderPlate(PlateContent plateContent, ScreeningViewContext viewContext)
+ /** @return widget with plate visualization - all the wells and possibility to browse images. */
+ public static Widget createVisualization(PlateImages plateImages,
+ ScreeningViewContext viewContext)
{
- LayoutContainer container = new LayoutContainer();
- Widget datasetNumberLegend = tryRenderImageDatasetsNumberLegend(plateContent, viewContext);
- if (datasetNumberLegend != null)
- {
- container.add(datasetNumberLegend);
- }
- container.add(renderWellsMatrix(plateContent, viewContext));
+ final LayoutContainer container = new LayoutContainer();
+ container.setLayout(new RowLayout());
+ LayoutContainer wellsMatrix = renderWellsMatrix(plateImages, viewContext);
+ container.add(wellsMatrix);
container.add(renderWellsLegend());
-
- add(container, createMarginLayoutData());
+ return container;
}
- private Widget tryRenderImageDatasetsNumberLegend(PlateContent plateContent,
- IViewContext<?> viewContext)
- {
- int datasetsNumber = plateContent.getImageDatasetsNumber();
- if (datasetsNumber == 0)
- {
- return new Text("No images data is available.");
- } else if (datasetsNumber == 1)
- {
- return null;
- } else
- {
- return new Text("There are " + datasetsNumber + " datasets with images, "
- + "select the one of your interest from the 'Data Sets' section "
- + "and go to its detail view to browse acquired images.");
- }
- }
-
- private RowData createMarginLayoutData()
- {
- RowData layoutData = new RowData();
- layoutData.setMargins(new Margins(10));
- return layoutData;
- }
-
- private LayoutContainer renderWellsLegend()
- {
- LayoutContainer legend = new LayoutContainer();
- legend.setLayout(new TableLayout(2));
-
- TableData mergedColumns = new TableData();
- mergedColumns.setColspan(2);
-
- Component verticalSeparator = createBox();
- verticalSeparator.setHeight("10");
- legend.add(verticalSeparator, mergedColumns);
-
- legend.add(new Text("Put a mouse on a well or click on it to get the details."),
- mergedColumns);
- legend.add(new Text("Legend:"), mergedColumns);
-
- legend.add(createNonEmptyWell(false));
- legend.add(new Text("Non-empty well"));
-
- legend.add(createNonEmptyWell(true));
- legend.add(new Text("Control well"));
-
- legend.add(createEmptyWellWidget());
- legend.add(new Text("Empty well"));
-
- return legend;
- }
-
- private LayoutContainer renderWellsMatrix(PlateContent plateContent,
+ private static LayoutContainer renderWellsMatrix(PlateImages plateContent,
ScreeningViewContext viewContext)
{
WellData[][] wellMatrix = createMatrix(plateContent);
@@ -250,7 +94,7 @@ public class PlateLayoutSection extends SingleSectionPanel
}
private static List<Widget> createWellWidgets(WellData[][] wellMatrix,
- PlateContent plateContent, ScreeningViewContext viewContext)
+ PlateImages plateContent, ScreeningViewContext viewContext)
{
List<Widget> wellWidgets = new ArrayList<Widget>();
int rowsNum = wellMatrix.length;
@@ -324,7 +168,33 @@ public class PlateLayoutSection extends SingleSectionPanel
}
}
- // ------ end todo
+ private static LayoutContainer renderWellsLegend()
+ {
+ LayoutContainer legend = new LayoutContainer();
+ legend.setLayout(new TableLayout(2));
+
+ TableData mergedColumns = new TableData();
+ mergedColumns.setColspan(2);
+
+ Component verticalSeparator = createBox();
+ verticalSeparator.setHeight("10");
+ legend.add(verticalSeparator, mergedColumns);
+
+ legend.add(new Text("Put a mouse on a well or click on it to get the details."),
+ mergedColumns);
+ legend.add(new Text("Legend:"), mergedColumns);
+
+ legend.add(createNonEmptyWell(false));
+ legend.add(new Text("Non-empty well"));
+
+ legend.add(createNonEmptyWell(true));
+ legend.add(new Text("Control well"));
+
+ legend.add(createEmptyWellWidget());
+ legend.add(new Text("Empty well"));
+
+ return legend;
+ }
private static Component createEmptyWellWidget()
{
@@ -334,7 +204,7 @@ public class PlateLayoutSection extends SingleSectionPanel
}
private static Component createWellWidget(final WellData wellData,
- final PlateContent plateContent, final DefaultChannelState channelState,
+ final PlateImages plateContent, final DefaultChannelState channelState,
final ScreeningViewContext viewContext)
{
Component widget = createContentWell(wellData);
@@ -416,7 +286,7 @@ public class PlateLayoutSection extends SingleSectionPanel
// Elements will not contain null even if well is empty.
// Numbering starts with 1 so row and column with index 0 are left empty.
- private static WellData[][] createMatrix(PlateContent plateContent)
+ private static WellData[][] createMatrix(PlateImages plateContent)
{
WellData[][] matrix = createWellData(plateContent);
List<WellMetadata> wells = plateContent.getWells();
@@ -432,7 +302,7 @@ public class PlateLayoutSection extends SingleSectionPanel
return matrix;
}
- private static WellData[][] createWellData(PlateContent plateContent)
+ private static WellData[][] createWellData(PlateImages plateContent)
{
WellData[][] data =
new WellData[plateContent.getRowsNum() + 1][plateContent.getColsNum() + 1];
@@ -446,41 +316,53 @@ public class PlateLayoutSection extends SingleSectionPanel
return data;
}
- private void addMetadataTable(final PlateContent plateContent,
+ // ---------
+
+ /** @return a button which shows a grid with the plate metadata */
+ public static Button createPlateMetadataButton(final Sample plate,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
- final Button generateButton =
- new Button("Show Plate Report", new SelectionListener<ButtonEvent>()
- {
+ return new Button("Show Plate Report", new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ DispatcherHelper.dispatchNaviEvent(createPlateMetadataTabFactory());
+ }
- @Override
- public void componentSelected(ButtonEvent ce)
+ private ITabItemFactory createPlateMetadataTabFactory()
+ {
+ return new ITabItemFactory()
{
- final ITabItemFactory tabFactory = new ITabItemFactory()
- {
- public ITabItem create()
- {
- return DefaultTabItem.create("Plate Report: "
- + plateContent.getPlate().getCode(),
- PlateMetadataBrowser.create(viewContext, sampleId),
- viewContext);
- }
-
- public String getId()
- {
- return GenericConstants.ID_PREFIX + "plate-metadata-"
- + plateContent.getPlate().getId();
- }
-
- public HelpPageIdentifier getHelpPageIdentifier()
- {
- return new HelpPageIdentifier(HelpPageDomain.SAMPLE,
- HelpPageAction.VIEW);
- }
- };
- DispatcherHelper.dispatchNaviEvent(tabFactory);
- }
- });
- add(generateButton, createMarginLayoutData());
+ public ITabItem create()
+ {
+ return DefaultTabItem.create("Plate Report: " + plate.getCode(),
+ PlateMetadataBrowser.create(viewContext, new TechId(plate
+ .getId())), viewContext);
+ }
+
+ public String getId()
+ {
+ return GenericConstants.ID_PREFIX + "plate-metadata-"
+ + plate.getId();
+ }
+
+ public HelpPageIdentifier getHelpPageIdentifier()
+ {
+ return new HelpPageIdentifier(HelpPageDomain.SAMPLE,
+ HelpPageAction.VIEW);
+ }
+ };
+ }
+ });
+ }
+
+ /** @return layout data with big margin */
+ public static RowData createRowLayoutMarginData()
+ {
+ RowData layoutData = new RowData();
+ layoutData.setMargins(new Margins(10));
+ return layoutData;
}
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateSampleViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateSampleViewer.java
index 6dbd98312f6..5ff75844edd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateSampleViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateSampleViewer.java
@@ -64,7 +64,7 @@ public final class PlateSampleViewer extends GenericSampleViewer
protected List<SingleSectionPanel> createAdditionalSectionPanels()
{
List<SingleSectionPanel> sections = new ArrayList<SingleSectionPanel>();
- sections.add(new PlateLayoutSection(screeningViewContext, sampleId));
+ sections.add(new PlateLayoutSampleSection(screeningViewContext, sampleId));
return sections;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellData.java
index 9503d5a496d..8aa5bb1c779 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellData.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellData.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
@@ -35,21 +35,21 @@ class WellData
private ExperimentIdentifier experimentIdentifier;
- public static WellData create(PlateContent plateContent, WellLocation location)
+ public static WellData create(PlateImages plateImages, WellLocation location)
{
- ExperimentIdentifier experimentIdentifier = getExperimentIdentifier(plateContent);
- WellImages wellImages = tryCreateWellImages(plateContent, location);
+ ExperimentIdentifier experimentIdentifier = getExperimentIdentifier(plateImages);
+ WellImages wellImages = tryCreateWellImages(plateImages, location);
return new WellData(wellImages, experimentIdentifier);
}
- private static ExperimentIdentifier getExperimentIdentifier(PlateContent plateContent)
+ private static ExperimentIdentifier getExperimentIdentifier(PlateImages plateImages)
{
- return ExperimentIdentifier.createIdentifier(plateContent.getPlate().getExperiment());
+ return ExperimentIdentifier.createIdentifier(plateImages.getPlate().getExperiment());
}
- private static WellImages tryCreateWellImages(PlateContent plateContent, WellLocation location)
+ private static WellImages tryCreateWellImages(PlateImages plateImages, WellLocation location)
{
- DatasetImagesReference images = plateContent.tryGetImages();
+ DatasetImagesReference images = plateImages.tryGetImages();
if (images != null)
{
return new WellImages(images.getImageParameters(), images.getDownloadUrl(), location);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java
index 321653f6050..3fdb09cdd64 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/PlateMetadataProvider.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
/**
* Original data provider for plate content.
- *
+ *
* @author Izabela Adamczyk
*/
class PlateMetadataProvider implements IOriginalDataProvider<GenericTableRow>
@@ -51,7 +51,7 @@ class PlateMetadataProvider implements IOriginalDataProvider<GenericTableRow>
public PlateMetadataProvider(IScreeningServer server, String sessionToken, TechId plateId)
{
plateContent = server.getPlateContent(sessionToken, plateId);
- wells = plateContent.getWells();
+ wells = plateContent.getPlateImages().getWells();
}
public List<GenericTableRow> getOriginalData() throws UserFailureException
@@ -89,34 +89,39 @@ class PlateMetadataProvider implements IOriginalDataProvider<GenericTableRow>
{
List<Column> columns = new ArrayList<Column>();
Column codeColumn =
- new Column(GenericTableColumnHeader.untitledLinkableStringHeader(PlateMetadataStaticColumns.WELL
- .ordinal(), PlateMetadataStaticColumns.WELL.colId()));
+ new Column(GenericTableColumnHeader.untitledLinkableStringHeader(
+ PlateMetadataStaticColumns.WELL.ordinal(), PlateMetadataStaticColumns.WELL
+ .colId()));
columns.add(codeColumn);
Column typeColumn =
- new Column(GenericTableColumnHeader.untitledStringHeader(PlateMetadataStaticColumns.TYPE
- .ordinal(), PlateMetadataStaticColumns.TYPE.colId()));
+ new Column(GenericTableColumnHeader.untitledStringHeader(
+ PlateMetadataStaticColumns.TYPE.ordinal(), PlateMetadataStaticColumns.TYPE
+ .colId()));
columns.add(typeColumn);
Column contentColumn =
new Column(GenericTableColumnHeader.untitledLinkableStringHeader(
- PlateMetadataStaticColumns.CONTENT.ordinal(), PlateMetadataStaticColumns.CONTENT.colId()));
+ PlateMetadataStaticColumns.CONTENT.ordinal(),
+ PlateMetadataStaticColumns.CONTENT.colId()));
columns.add(contentColumn);
Column contentTypeColumn =
- new Column(GenericTableColumnHeader.untitledStringHeader(PlateMetadataStaticColumns.CONTENT_TYPE
- .ordinal(), PlateMetadataStaticColumns.CONTENT_TYPE.colId()));
+ new Column(GenericTableColumnHeader.untitledStringHeader(
+ PlateMetadataStaticColumns.CONTENT_TYPE.ordinal(),
+ PlateMetadataStaticColumns.CONTENT_TYPE.colId()));
columns.add(contentTypeColumn);
Column geneCodeColumn =
new Column(GenericTableColumnHeader.untitledLinkableStringHeader(
- PlateMetadataStaticColumns.INHIBITED_GENE.ordinal(), PlateMetadataStaticColumns.INHIBITED_GENE
- .colId()));
+ PlateMetadataStaticColumns.INHIBITED_GENE.ordinal(),
+ PlateMetadataStaticColumns.INHIBITED_GENE.colId()));
columns.add(geneCodeColumn);
Column showGeneColumn =
new Column(GenericTableColumnHeader.untitledLinkableStringHeader(
- PlateMetadataStaticColumns.GENE_DETAILS.ordinal(), PlateMetadataStaticColumns.GENE_DETAILS.colId()));
+ PlateMetadataStaticColumns.GENE_DETAILS.ordinal(),
+ PlateMetadataStaticColumns.GENE_DETAILS.colId()));
columns.add(showGeneColumn);
int fixedColumns = columns.size();
PropertyColumns contentPropertyColumns = new PropertyColumns();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
index ab8d5618d83..6c7aad01fe9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningCli
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.PlateContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
/**
@@ -137,6 +138,17 @@ public final class ScreeningClientService extends AbstractClientService implemen
}
}
+ public PlateImages getPlateContentForDataset(TechId datasetId)
+ {
+ try
+ {
+ return server.getPlateContentForDataset(getSessionToken(), datasetId);
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
public List<WellContent> getPlateLocations(TechId geneMaterialId,
ExperimentIdentifier experimentIdentifier) throws UserFailureException
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
index 31d2d18fbf6..43ab486ff28 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
@@ -42,4 +43,6 @@ public interface IScreeningBusinessObjectFactory
public ISampleLister createSampleLister(Session session);
public IMaterialLister createMaterialLister(Session session);
+
+ public IExternalDataBO createExternalDataBO(Session session);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
index 64116aed338..be2fdc699e5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server;
import org.springframework.stereotype.Component;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
@@ -68,4 +69,9 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
return getCommonBusinessObjectFactory().createMaterialBO(session);
}
+ public IExternalDataBO createExternalDataBO(Session session)
+ {
+ return getCommonBusinessObjectFactory().createExternalDataBO(session);
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 0a7ee7b2587..c5e42a75b7f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -46,6 +46,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader
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.PlateContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
/**
@@ -122,6 +123,12 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return PlateContentLoader.load(session, businessObjectFactory, plateId);
}
+ public PlateImages getPlateContentForDataset(String sessionToken, TechId datasetId)
+ {
+ Session session = getSession(sessionToken);
+ return PlateContentLoader.loadForDataset(session, businessObjectFactory, datasetId);
+ }
+
public List<WellContent> getPlateLocations(String sessionToken, TechId geneMaterialId,
ExperimentIdentifier experimentIdentifier)
{
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 0fc49e47606..7513e7970f9 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
@@ -31,6 +31,7 @@ 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.shared.IScreeningServer;
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.WellContent;
/**
@@ -62,28 +63,33 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
public PlateContent getPlateContent(String sessionToken, TechId plateId)
{
- logTracking(sessionToken, "getPlateContent", "PLATE(%s)", plateId.getId());
+ logAccess(sessionToken, "getPlateContent", "PLATE(%s)", plateId.getId());
+ return null;
+ }
+
+ public PlateImages getPlateContentForDataset(String sessionToken, TechId datasetId)
+ {
+ logAccess(sessionToken, "getPlateContentForDataset", "DATASET(%s)", datasetId.getId());
return null;
}
public List<WellContent> getPlateLocations(String sessionToken, TechId geneMaterialId,
ExperimentIdentifier experimentIdentifier)
{
- logTracking(sessionToken, "getPlateLocations",
- "geneMaterialId(%s) experimentIdentifier(%s)", geneMaterialId.getId(),
- experimentIdentifier);
+ logAccess(sessionToken, "getPlateLocations", "geneMaterialId(%s) experimentIdentifier(%s)",
+ geneMaterialId.getId(), experimentIdentifier);
return null;
}
public Material getMaterialInfo(String sessionToken, TechId materialId)
{
- logTracking(sessionToken, "getMaterialInfo", "materialId(%s)", materialId.getId());
+ logAccess(sessionToken, "getMaterialInfo", "materialId(%s)", materialId.getId());
return null;
}
public ExternalData getDataSetInfo(String sessionToken, TechId datasetId)
{
- logTracking(sessionToken, "getDataSetInfo", "datasetId(%s)", datasetId.getId());
+ logAccess(sessionToken, "getDataSetInfo", "datasetId(%s)", datasetId.getId());
return null;
}
}
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 caa98fed997..161b24102cc 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
@@ -20,6 +20,8 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
@@ -41,6 +43,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReferen
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.DatasetImagesReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
@@ -51,12 +54,27 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
*/
public class PlateContentLoader
{
+ /**
+ * loads data about the plate for a specified sample id. Attaches information about images and
+ * image analysis only if one dataset with such a data exist.
+ */
public static PlateContent load(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, TechId plateId)
{
return new PlateContentLoader(session, businessObjectFactory).getPlateContent(plateId);
}
+ /**
+ * loads data about the plate for a specified dataset, which is supposed to contain images in
+ * BDS-HCS format.
+ */
+ public static PlateImages loadForDataset(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, TechId datasetId)
+ {
+ return new PlateContentLoader(session, businessObjectFactory)
+ .getPlateContentForDataset(datasetId);
+ }
+
private final Session session;
private final IScreeningBusinessObjectFactory businessObjectFactory;
@@ -68,6 +86,29 @@ public class PlateContentLoader
this.businessObjectFactory = businessObjectFactory;
}
+ private PlateImages getPlateContentForDataset(TechId datasetId)
+ {
+ ExternalDataPE externalData = loadDataset(datasetId);
+ SamplePE plate = externalData.tryGetSample();
+ if (plate == null)
+ {
+ throw UserFailureException.fromTemplate("Dataset '%s' has no sample connected.",
+ externalData.getCode());
+ }
+ List<WellMetadata> wells = loadWells(new TechId(plate.getId()));
+ DatasetImagesReference datasetImagesReference =
+ loadImages(businessObjectFactory.createExternalDataTable(session), externalData);
+ return new PlateImages(translate(plate), wells, datasetImagesReference);
+ }
+
+ private ExternalDataPE loadDataset(TechId datasetId)
+ {
+ IExternalDataBO externalDataBO = businessObjectFactory.createExternalDataBO(session);
+ externalDataBO.loadDataByTechId(datasetId);
+ ExternalDataPE externalData = externalDataBO.getExternalData();
+ return externalData;
+ }
+
private PlateContent getPlateContent(TechId plateId)
{
IExternalDataTable externalDataTable =
@@ -101,6 +142,11 @@ public class PlateContentLoader
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadDataByTechId(plateId);
SamplePE sample = sampleBO.getSample();
+ return translate(sample);
+ }
+
+ private Sample translate(SamplePE sample)
+ {
return SampleTranslator.translate(sample, session.getBaseIndexURL());
}
@@ -153,10 +199,12 @@ public class PlateContentLoader
return externalData;
}
- private DatasetImagesReference loadImages(IExternalDataTable externalDataTable, ExternalDataPE dataset)
+ private DatasetImagesReference loadImages(IExternalDataTable externalDataTable,
+ ExternalDataPE dataset)
{
PlateImageParameters imageParameters = loadImageParams(dataset, externalDataTable);
- return DatasetImagesReference.create(ScreeningUtils.createDatasetReference(dataset), imageParameters);
+ return DatasetImagesReference.create(ScreeningUtils.createDatasetReference(dataset),
+ imageParameters);
}
private PlateImageParameters loadImageParams(ExternalDataPE dataset,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
index 1458612628e..fd6bade5a70 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.GroupIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.DataSetTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
@@ -34,6 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
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.WellContent;
/**
@@ -51,6 +53,14 @@ public interface IScreeningServer extends IServer
public PlateContent getPlateContent(String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class) TechId plateId);
+ /**
+ * Returns plate content for a specified HCS_IMAGE dataset.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleSet.OBSERVER)
+ public PlateImages getPlateContentForDataset(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetTechIdPredicate.class) TechId datasetId);
+
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.OBSERVER)
public List<WellContent> getPlateLocations(
@@ -83,6 +93,6 @@ public interface IScreeningServer extends IServer
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleSet.OBSERVER)
- public ExternalData getDataSetInfo(String sessionToken, TechId datasetId);
-
+ public ExternalData getDataSetInfo(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetTechIdPredicate.class) TechId datasetId);
}
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 b3e3114cc8b..1add940049f 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
@@ -30,12 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
*/
public class PlateContent implements IsSerializable
{
- private Sample plate;
-
- private List<WellMetadata> wellsMetadata;
-
- // not null if exactly one image dataset exists
- private DatasetImagesReference imagesOrNull;
+ private PlateImages plateImages;
// not null if exactly one image analysis dataset exists
private DatasetReference imageAnalysisDatasetOrNull;
@@ -58,66 +53,34 @@ public class PlateContent implements IsSerializable
|| (imagesOrNull == null && imageDatasetsNumber != 1);
assert (imageAnalysisDatasetOrNull != null && imageAnalysisDatasetsNumber == 1)
|| (imageAnalysisDatasetOrNull == null && imageAnalysisDatasetsNumber != 1);
- this.plate = plate;
- this.wellsMetadata = wells;
- this.imagesOrNull = imagesOrNull;
+ this.plateImages = new PlateImages(plate, wells, imagesOrNull);
this.imageDatasetsNumber = imageDatasetsNumber;
this.imageAnalysisDatasetOrNull = imageAnalysisDatasetOrNull;
this.imageAnalysisDatasetsNumber = imageAnalysisDatasetsNumber;
}
- public List<WellMetadata> getWells()
- {
- return wellsMetadata;
- }
-
- /** can be null */
- public DatasetImagesReference tryGetImages()
- {
- return imagesOrNull;
- }
-
public DatasetReference tryGetImageAnalysisDataset()
{
return imageAnalysisDatasetOrNull;
}
- public Sample getPlate()
- {
- return plate;
- }
-
- public int getRowsNum()
+ public int getImageDatasetsNumber()
{
- if (imagesOrNull != null)
- {
- return imagesOrNull.getImageParameters().getRowsNum();
- } else
- {
- // TODO 2009-12-09, Tomasz Pylak: calculate rows number on the basis of metadata
- return 16;
- }
+ return imageDatasetsNumber;
}
- public int getColsNum()
+ public int getImageAnalysisDatasetsNumber()
{
- if (imagesOrNull != null)
- {
- return imagesOrNull.getImageParameters().getColsNum();
- } else
- {
- // TODO 2009-12-09, Tomasz Pylak: calculate rows number on the basis of metadata
- return 24;
- }
+ return imageAnalysisDatasetsNumber;
}
- public int getImageDatasetsNumber()
+ public PlateImages getPlateImages()
{
- return imageDatasetsNumber;
+ return plateImages;
}
- public int getImageAnalysisDatasetsNumber()
+ public Sample getPlate()
{
- return imageAnalysisDatasetsNumber;
+ return plateImages.getPlate();
}
}
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/PlateImages.java
new file mode 100644
index 00000000000..ec68f5d2727
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
@@ -0,0 +1,92 @@
+/*
+ * 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.shared.basic.dto;
+
+import java.util.List;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+
+/**
+ * DTO with metadata of a plate and all its wells + reference to a dataset with plate images.
+ *
+ * @author Tomasz Pylak
+ */
+public class PlateImages implements IsSerializable
+{
+ private Sample plate;
+
+ private List<WellMetadata> wellsMetadata;
+
+ // null if dataset with images does not exist
+ private DatasetImagesReference imagesOrNull;
+
+ // GWT only
+ @SuppressWarnings("unused")
+ private PlateImages()
+ {
+ }
+
+ public PlateImages(Sample plate, List<WellMetadata> wellsMetadata,
+ DatasetImagesReference imagesOrNull)
+ {
+ this.plate = plate;
+ this.wellsMetadata = wellsMetadata;
+ this.imagesOrNull = imagesOrNull;
+ }
+
+ public List<WellMetadata> getWells()
+ {
+ return wellsMetadata;
+ }
+
+ /** can be null */
+ public DatasetImagesReference tryGetImages()
+ {
+ return imagesOrNull;
+ }
+
+ public Sample getPlate()
+ {
+ return plate;
+ }
+
+ public int getRowsNum()
+ {
+ if (imagesOrNull != null)
+ {
+ return imagesOrNull.getImageParameters().getRowsNum();
+ } else
+ {
+ // TODO 2009-12-09, Tomasz Pylak: calculate rows number on the basis of metadata
+ return 16;
+ }
+ }
+
+ public int getColsNum()
+ {
+ if (imagesOrNull != null)
+ {
+ return imagesOrNull.getImageParameters().getColsNum();
+ } else
+ {
+ // TODO 2009-12-09, Tomasz Pylak: calculate rows number on the basis of metadata
+ return 24;
+ }
+ }
+}
--
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