From 5bcf8975966a0beb52e0dd325e749fbed966d773 Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Wed, 5 Oct 2011 09:26:37 +0000
Subject: [PATCH] LMS-2537 InfectX SpotFire integration: allow to link to well
images even if metadata for the well are missing
SVN: 23200
---
.../locator/PermlinkLocatorResolver.java | 2 +-
.../application/ClientPluginFactory.java | 61 ++++++++-
.../application/DisplayTypeIDGenerator.java | 2 +
.../application/ScreeningViewContext.java | 2 +
.../detailviewers/ImageDataSetSection.java | 109 +++++++++++++++
.../detailviewers/ImageDataSetViewer.java | 74 +++++++++++
.../detailviewers/ImageSampleSection.java | 65 ---------
.../detailviewers/LogicalImageLayouter.java | 72 ++++++++++
.../detailviewers/WellContentDialog.java | 71 +++++++---
.../ImagingDataSetLocatorResolver.java | 125 ++++++++++++++++++
.../api/v1/dto/PlateImageReference.java | 3 +-
.../dto/ImageDatasetEnrichedReference.java | 31 ++++-
.../shared/basic/dto/WellLocation.java | 10 ++
13 files changed, 535 insertions(+), 92 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetSection.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetViewer.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageLayouter.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingDataSetLocatorResolver.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/PermlinkLocatorResolver.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/PermlinkLocatorResolver.java
index 8354d5576f4..861c08b87df 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/PermlinkLocatorResolver.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/locator/PermlinkLocatorResolver.java
@@ -43,7 +43,7 @@ public class PermlinkLocatorResolver extends AbstractViewLocatorResolver
/**
* Open the entity details tab for the specified entity kind and permId.
*/
- private void openInitialEntityViewer(String entityKindValue, String permIdValue)
+ protected void openInitialEntityViewer(String entityKindValue, String permIdValue)
throws UserFailureException
{
EntityKind entityKind = getEntityKind(entityKindValue);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
index f1083106c93..d4d4a7cde29 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
@@ -54,9 +54,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.sample.GenericSampleViewer;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.dataset.GenericDataSetViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ExperimentAnalysisSummaryViewer;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImageDataSetViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImageSampleViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImagingMaterialViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.MaterialFeaturesFromAllExperimentsViewer;
@@ -67,6 +68,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.sample.LibrarySampleBatchRegistrationForm;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchByProjectCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
@@ -156,7 +158,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
}
if (EntityKind.DATA_SET.equals(entityKind))
{
- return (IClientPlugin<T, I>) new DatasetClientPlugin(viewContext);
+ return (IClientPlugin<T, I>) new createImageDataSetViewer(viewContext);
}
throw new UnsupportedOperationException("IClientPlugin for entity kind '" + entityKind
+ "' not implemented yet.");
@@ -342,22 +344,67 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
};
}
- private final class DatasetClientPlugin extends DelegatedClientPlugin<DataSetType>
+ private final class createImageDataSetViewer extends DelegatedClientPlugin<DataSetType>
{
private final ScreeningViewContext screeningViewContext;
- private DatasetClientPlugin(ScreeningViewContext viewContext)
+ private createImageDataSetViewer(ScreeningViewContext viewContext)
{
super(viewContext, EntityKind.DATA_SET);
this.screeningViewContext = viewContext;
}
+ private AbstractTabItemFactory createImageDataSetViewer(
+ final IEntityInformationHolderWithPermId entity, final WellLocation wellLocation)
+ {
+ return new AbstractTabItemFactory()
+ {
+ @Override
+ public ITabItem create()
+ {
+ final DatabaseModificationAwareComponent viewer =
+ ImageDataSetViewer.create(screeningViewContext, entity,
+ wellLocation);
+ return createViewerTab(viewer, getTabTitle(), screeningViewContext);
+ }
+
+ @Override
+ public String getId()
+ {
+ final TechId dataSetId = TechId.create(entity);
+ return GenericDataSetViewer.createId(dataSetId);
+ }
+
+ @Override
+ public HelpPageIdentifier getHelpPageIdentifier()
+ {
+ return HelpPageIdentifier.createSpecific("Plate Well Viewer");
+ }
+
+ @Override
+ public String getTabTitle()
+ {
+ return getViewerTitle(Dict.WELL, entity, screeningViewContext);
+ }
+
+ @Override
+ public String tryGetLink()
+ {
+ return LinkExtractor.tryExtract(entity);
+ }
+ };
+ }
+
@Override
public final AbstractTabItemFactory createEntityViewer(
final IEntityInformationHolderWithPermId entity)
{
String datasetTypeCode = entity.getEntityType().getCode();
- if (datasetTypeCode.matches(ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN))
+ if (entity.getPermId().contains(":"))
+ {
+ return createImageDataSetViewer(entity, new WellLocation(1, 1));
+ } else if (datasetTypeCode
+ .matches(ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN))
{
return createHCSImageDatasetTabItemFactory(entity);
} else if (datasetTypeCode
@@ -502,7 +549,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
public String getId()
{
final TechId sampleId = TechId.create(entity);
- return GenericSampleViewer.createId(sampleId);
+ return GenericDataSetViewer.createId(sampleId);
}
@Override
@@ -548,7 +595,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
public String getId()
{
final TechId sampleId = TechId.create(entity);
- return GenericSampleViewer.createId(sampleId);
+ return GenericDataSetViewer.createId(sampleId);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java
index 5ffc9eb5447..b4363ba6d19 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/DisplayTypeIDGenerator.java
@@ -33,6 +33,8 @@ public enum DisplayTypeIDGenerator implements IDisplayTypeIDGenerator
LOGICAL_IMAGE_DATASET_SECTION("logical-image-dataset-section"),
+ LOGICAL_IMAGE_WELL_DATASET_SECTION("logical-image-well-dataset-section"),
+
PLATE_LOCATIONS_MATERIAL_SECTION("plate-locations-material-section"),
EXPERIMENT_PLATE_LOCATIONS_SECTION("plate-locations-experiment-section"),
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java
index 51c2651bf6c..383bc05e91a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java
@@ -10,6 +10,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningCli
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.ExperimentAnalysisSummaryResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.GlobalWellSearchLocatorResolver;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.ImagingDataSetLocatorResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.ImagingMaterialLocatorResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.PlateMetadataBrowserLocatorResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.WellSearchLocatorResolver;
@@ -45,6 +46,7 @@ public final class ScreeningViewContext extends
{
super.initializeLocatorHandlerRegistry(handlerRegistry);
+ handlerRegistry.registerHandler(new ImagingDataSetLocatorResolver(this));
handlerRegistry.registerHandler(new ImagingMaterialLocatorResolver(this));
handlerRegistry.registerHandler(new PlateMetadataBrowserLocatorResolver(this));
handlerRegistry.registerHandler(new WellSearchLocatorResolver(this));
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetSection.java
new file mode 100644
index 00000000000..065444117b4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetSection.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2011 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.Collections;
+
+import com.extjs.gxt.ui.client.Style.Scroll;
+import com.extjs.gxt.ui.client.widget.Text;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+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.TabContent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.DisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.heatmaps.LayoutUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ImageDataSetSection extends TabContent
+{
+ private final ExternalData dataSet;
+
+ private final WellLocation wellLocationOrNull;
+
+ private static final String WELL_IMAGE_SECTION_TITLE_PREFIX = "Well ";
+
+ private static final String WELL_IMAGE_SECTION_TITLE_SUFFIX = " Images";
+
+ public ImageDataSetSection(final ScreeningViewContext viewContext, final ExternalData dataSet,
+ WellLocation wellLocationOrNull)
+ {
+ super(WELL_IMAGE_SECTION_TITLE_PREFIX
+ + (wellLocationOrNull == null ? "" : wellLocationOrNull.toWellIdString())
+ + WELL_IMAGE_SECTION_TITLE_SUFFIX, viewContext, dataSet);
+
+ this.dataSet = dataSet;
+ this.wellLocationOrNull = wellLocationOrNull;
+ setIds(DisplayTypeIDGenerator.LOGICAL_IMAGE_WELL_DATASET_SECTION);
+ }
+
+ private ScreeningViewContext getViewContext()
+ {
+ return (ScreeningViewContext) viewContext;
+ }
+
+ @Override
+ protected void showContent()
+ {
+ final ScreeningViewContext context = getViewContext();
+ add(new Text(context.getMessage(Dict.LOAD_IN_PROGRESS)));
+ context.getService().getImageDatasetInfo(dataSet.getCode(),
+ dataSet.getDataStore().getCode(), wellLocationOrNull,
+ createDisplayImagesCallback(context));
+ }
+
+ private AsyncCallback<LogicalImageInfo> createDisplayImagesCallback(ScreeningViewContext context)
+ {
+ return new AbstractAsyncCallback<LogicalImageInfo>(context)
+ {
+ @Override
+ protected void process(LogicalImageInfo imageDataSet)
+ {
+ removeAll();
+ setLayout(new RowLayout());
+ setScrollMode(Scroll.AUTO);
+
+ addVisualisation(imageDataSet);
+ layout();
+ }
+ };
+ }
+
+ private void addVisualisation(LogicalImageInfo imageDataSet)
+ {
+ RowData margins = LayoutUtils.createRowLayoutSurroundingData();
+
+ final ScreeningViewContext context = getViewContext();
+ final LogicalImageLayouter logicalImageLayouter =
+ new LogicalImageLayouter(context, wellLocationOrNull,
+ Collections.singletonList(imageDataSet));
+
+ ImageDatasetEnrichedReference firstImageDataset = imageDataSet.getImageDataset();
+ logicalImageLayouter.changeDisplayedImageDataset(firstImageDataset);
+
+ add(logicalImageLayouter, margins);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetViewer.java
new file mode 100644
index 00000000000..f27ea4b7390
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageDataSetViewer.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.dataset.GenericDataSetViewer;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ImageDataSetViewer extends GenericDataSetViewer
+{
+ public static DatabaseModificationAwareComponent create(final ScreeningViewContext viewContext,
+ final IIdAndCodeHolder identifiable, WellLocation wellLocationOrNull)
+ {
+ ImageDataSetViewer viewer =
+ new ImageDataSetViewer(viewContext, identifiable, wellLocationOrNull);
+ viewer.reloadAllData();
+ return new DatabaseModificationAwareComponent(viewer, viewer);
+ }
+
+ private final ScreeningViewContext screeningViewContext;
+
+ private final WellLocation wellLocationOrNull;
+
+ protected ImageDataSetViewer(ScreeningViewContext screeningViewContext,
+ IIdAndCodeHolder identifiable, WellLocation wellLocationOrNull)
+ {
+ super(screeningViewContext, identifiable);
+
+ this.screeningViewContext = screeningViewContext;
+ this.wellLocationOrNull = wellLocationOrNull;
+ }
+
+ @Override
+ protected List<TabContent> createAdditionalSectionPanels(ExternalData dataset)
+ {
+ List<TabContent> sections = new ArrayList<TabContent>();
+
+ sections.add(new ImageDataSetSection(screeningViewContext, dataset, wellLocationOrNull));
+ return sections;
+ }
+
+ @Override
+ protected void loadDatasetInfo(TechId datasetTechId, AsyncCallback<ExternalData> asyncCallback)
+ {
+ screeningViewContext.getService().getDataSetInfo(datasetTechId, asyncCallback);
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageSampleSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageSampleSection.java
index fbf6adca39a..3d79891c6a4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageSampleSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageSampleSection.java
@@ -16,13 +16,9 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
-import java.util.ArrayList;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
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.RowData;
import com.extjs.gxt.ui.client.widget.layout.RowLayout;
@@ -35,8 +31,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.DisplayTypeIDGenerator;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImagingDatasetGuiUtils.IDatasetImagesReferenceUpdater;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.heatmaps.LayoutUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
@@ -142,63 +136,4 @@ public class ImageSampleSection extends TabContent
add(logicalImageLayouter, margins);
}
}
-
- private static class LogicalImageLayouter extends LayoutContainer implements
- IDatasetImagesReferenceUpdater
- {
- private final ScreeningViewContext viewContext;
-
- private final WellLocation wellLocationOrNull;
-
- private final Map<ImageDatasetEnrichedReference, LogicalImageInfo> refsMap;
-
- public LogicalImageLayouter(ScreeningViewContext viewContext,
- WellLocation wellLocationOrNull, List<LogicalImageInfo> images)
- {
- this.viewContext = viewContext;
- this.wellLocationOrNull = wellLocationOrNull;
- this.refsMap = createRefsMap(images);
- }
-
- public void changeDisplayedImageDataset(ImageDatasetEnrichedReference dataset)
- {
- LogicalImageInfo imageInfo = refsMap.get(dataset);
- assert imageInfo != null : "cannot find logical image for " + dataset;
-
- removeAll();
- Widget viewerWidget = createImageViewer(imageInfo);
- add(viewerWidget);
- layout();
- }
-
- private Widget createImageViewer(LogicalImageInfo imageInfo)
- {
- LogicalImageReference logicalImageReference =
- new LogicalImageReference(imageInfo.getImageDataset(), wellLocationOrNull);
- LogicalImageViewer viewer =
- new LogicalImageViewer(logicalImageReference, viewContext,
- imageInfo.getExperimentIdentifier(), imageInfo.getExperimentPermId(),
- true);
- return viewer.getViewerWidget(imageInfo.getChannelStacks());
- }
-
- public List<ImageDatasetEnrichedReference> getDatasetImagesReferences()
- {
- return new ArrayList<ImageDatasetEnrichedReference>(refsMap.keySet());
- }
-
- private static Map<ImageDatasetEnrichedReference, LogicalImageInfo> createRefsMap(
- List<LogicalImageInfo> images)
- {
- Map<ImageDatasetEnrichedReference, LogicalImageInfo> map =
- new HashMap<ImageDatasetEnrichedReference, LogicalImageInfo>();
- for (LogicalImageInfo imageInfo : images)
- {
- ImageDatasetEnrichedReference ref = imageInfo.getImageDataset();
- map.put(ref, imageInfo);
- }
- return map;
- }
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageLayouter.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageLayouter.java
new file mode 100644
index 00000000000..9c8f3f46100
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LogicalImageLayouter.java
@@ -0,0 +1,72 @@
+package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.google.gwt.user.client.ui.Widget;
+
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ImagingDatasetGuiUtils.IDatasetImagesReferenceUpdater;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+public class LogicalImageLayouter extends LayoutContainer implements IDatasetImagesReferenceUpdater
+{
+ private final ScreeningViewContext viewContext;
+
+ private final WellLocation wellLocationOrNull;
+
+ private final Map<ImageDatasetEnrichedReference, LogicalImageInfo> refsMap;
+
+ public LogicalImageLayouter(ScreeningViewContext viewContext, WellLocation wellLocationOrNull,
+ List<LogicalImageInfo> images)
+ {
+ this.viewContext = viewContext;
+ this.wellLocationOrNull = wellLocationOrNull;
+ this.refsMap = createRefsMap(images);
+ }
+
+ public void changeDisplayedImageDataset(ImageDatasetEnrichedReference dataset)
+ {
+ LogicalImageInfo imageInfo = refsMap.get(dataset);
+ assert imageInfo != null : "cannot find logical image for " + dataset;
+
+ removeAll();
+ Widget viewerWidget = createImageViewer(imageInfo);
+ add(viewerWidget);
+ layout();
+ }
+
+ private Widget createImageViewer(LogicalImageInfo imageInfo)
+ {
+ LogicalImageReference logicalImageReference =
+ new LogicalImageReference(imageInfo.getImageDataset(), wellLocationOrNull);
+ LogicalImageViewer viewer =
+ new LogicalImageViewer(logicalImageReference, viewContext,
+ imageInfo.getExperimentIdentifier(), imageInfo.getExperimentPermId(), true);
+ return viewer.getViewerWidget(imageInfo.getChannelStacks());
+ }
+
+ public List<ImageDatasetEnrichedReference> getDatasetImagesReferences()
+ {
+ return new ArrayList<ImageDatasetEnrichedReference>(refsMap.keySet());
+ }
+
+ private static Map<ImageDatasetEnrichedReference, LogicalImageInfo> createRefsMap(
+ List<LogicalImageInfo> images)
+ {
+ Map<ImageDatasetEnrichedReference, LogicalImageInfo> map =
+ new HashMap<ImageDatasetEnrichedReference, LogicalImageInfo>();
+ for (LogicalImageInfo imageInfo : images)
+ {
+ ImageDatasetEnrichedReference ref = imageInfo.getImageDataset();
+ map.put(ref, imageInfo);
+ }
+ return map;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
index 6c19502c692..cffa9878d0c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
@@ -48,6 +48,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewConte
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.listener.OpenEntityDetailsTabClickListener;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
@@ -77,8 +79,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCrit
*/
public class WellContentDialog extends Dialog
{
- private static final String UNKNOWN_WELL_LABEL = "No well information available.";
-
private static final String UNKNOWN_CHANNEL_LABEL = "No images available for this channel.";
private static final String INCORRECT_WELL_CODE_LABEL = "Incorrect well code.";
@@ -96,17 +96,17 @@ public class WellContentDialog extends Dialog
ImageDatasetEnrichedReference imageDatasetOrNull,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
- final WellContentDialog contentDialog = createContentDialog(wellData, viewContext);
- showContentDialog(contentDialog, imageDatasetOrNull, viewContext);
+ final WellContentDialog contentDialog =
+ createContentDialog(wellData, imageDatasetOrNull, viewContext);
+ showContentDialog(contentDialog, viewContext);
}
private static void showContentDialog(final WellContentDialog contentDialog,
- final ImageDatasetEnrichedReference imagesOrNull,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
- if (imagesOrNull != null)
+ if (contentDialog.tryGetImages() != null)
{
- LogicalImageViewer viewer = contentDialog.createImageViewer(imagesOrNull);
+ LogicalImageViewer viewer = contentDialog.createImageViewer();
contentDialog.add(viewer.getViewerWidget());
contentDialog.addImageEditorLaunchButton(viewer);
}
@@ -114,6 +114,7 @@ public class WellContentDialog extends Dialog
}
private static WellContentDialog createContentDialog(final WellData wellData,
+ ImageDatasetEnrichedReference imageDatasetOrNull,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
WellLocation wellLocation = wellData.getWellLocation();
@@ -126,7 +127,7 @@ public class WellContentDialog extends Dialog
wellPropertiesOrNull = wellMetadata.getWellSample().getProperties();
}
return new WellContentDialog(wellOrNull, wellPropertiesOrNull, wellLocation,
- getExperiment(wellData), viewContext);
+ getExperiment(wellData), imageDatasetOrNull, viewContext);
}
/**
@@ -200,12 +201,12 @@ public class WellContentDialog extends Dialog
{
WellContentDialog contentDialog =
new WellContentDialog(wellImage.getWell(), null, wellImage.tryGetLocation(),
- getExperiment(wellImage.getExperiment()), viewContext);
+ getExperiment(wellImage.getExperiment()), imageDatasetOrNull, viewContext);
- showContentDialog(contentDialog, imageDatasetOrNull, viewContext);
+ showContentDialog(contentDialog, viewContext);
}
- private LogicalImageViewer createImageViewer(ImageDatasetEnrichedReference imageDatasetOrNull)
+ private LogicalImageViewer createImageViewer()
{
final LogicalImageReference imagesOrNull =
new LogicalImageReference(imageDatasetOrNull, wellLocationOrNull);
@@ -245,9 +246,12 @@ public class WellContentDialog extends Dialog
private final IViewContext<IScreeningClientServiceAsync> viewContext;
+ private ImageDatasetEnrichedReference imageDatasetOrNull;
+
private WellContentDialog(IEntityInformationHolderWithPermId wellOrNull,
List<IEntityProperty> wellPropertiesOrNull, final WellLocation wellLocationOrNull,
final SingleExperimentSearchCriteria experimentCriteria,
+ ImageDatasetEnrichedReference imageDatasetOrNull,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
this.wellOrNull = wellOrNull;
@@ -258,6 +262,7 @@ public class WellContentDialog extends Dialog
Collections.sort(wellPropertiesOrNull);
}
this.experimentCriteria = experimentCriteria;
+ this.imageDatasetOrNull = imageDatasetOrNull;
this.viewContext = viewContext;
setScrollMode(Scroll.AUTO);
setHideOnButtonClick(true);
@@ -287,6 +292,11 @@ public class WellContentDialog extends Dialog
});
}
+ private ImageDatasetEnrichedReference tryGetImages()
+ {
+ return imageDatasetOrNull;
+ }
+
private void addImageEditorLaunchButton(final LogicalImageViewer viewer)
{
if (viewer.isImageEditorEnabled() == false)
@@ -327,10 +337,41 @@ public class WellContentDialog extends Dialog
if (wellOrNull != null)
{
container.add(new Text(WELL_LABEL), cellLayout);
- container.add(createEntityLink(wellOrNull));
+ container.add(createEntityLink(wellOrNull, wellOrNull.getCode()));
} else
{
- container.add(new Text(UNKNOWN_WELL_LABEL));
+ container.add(new Text(WELL_LABEL), cellLayout);
+ final String suffix =
+ wellLocationOrNull == null ? "" : ":" + wellLocationOrNull.toWellIdString();
+ container.add(createEntityLink(new IEntityInformationHolderWithPermId()
+ {
+ private static final long serialVersionUID = 1L;
+
+ public String getPermId()
+ {
+ return imageDatasetOrNull.getPermId() + suffix;
+ }
+
+ public String getCode()
+ {
+ return imageDatasetOrNull.getCode();
+ }
+
+ public Long getId()
+ {
+ return imageDatasetOrNull.getId();
+ }
+
+ public BasicEntityType getEntityType()
+ {
+ return imageDatasetOrNull.getEntityType();
+ }
+
+ public EntityKind getEntityKind()
+ {
+ return imageDatasetOrNull.getEntityKind();
+ }
+ }, getWellDescription()));
}
if (wellPropertiesOrNull != null)
{
@@ -459,10 +500,10 @@ public class WellContentDialog extends Dialog
return ExperimentSearchCriteria.createExperiment(experimentCriteria, false);
}
- private Widget createEntityLink(IEntityInformationHolderWithPermId entity)
+ private Widget createEntityLink(IEntityInformationHolderWithPermId entity, String label)
{
final ClickHandler listener = new OpenEntityDetailsTabClickListener(entity, viewContext);
- return LinkRenderer.getLinkWidget(entity.getCode(), listener);
+ return LinkRenderer.getLinkWidget(label, listener);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingDataSetLocatorResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingDataSetLocatorResolver.java
new file mode 100644
index 00000000000..cfe928b6510
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingDataSetLocatorResolver.java
@@ -0,0 +1,125 @@
+/*
+ * Copyright 2011 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.locator;
+
+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.locator.PermlinkLocatorResolver;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.listener.OpenEntityDetailsTabAction;
+import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ImagingDataSetLocatorResolver extends PermlinkLocatorResolver
+{
+ private final IViewContext<IScreeningClientServiceAsync> viewContext;
+
+ public ImagingDataSetLocatorResolver(IViewContext<IScreeningClientServiceAsync> viewContext)
+ {
+ super(viewContext.getCommonViewContext());
+ this.viewContext = viewContext;
+ }
+
+ @Override
+ public boolean canHandleLocator(ViewLocator locator)
+ {
+ String entityKindValueOrNull = locator.tryGetEntity();
+ String permIdValueOrNull =
+ locator.getParameters().get(PermlinkUtilities.PERM_ID_PARAMETER_KEY);
+
+ return super.canHandleLocator(locator)
+ && EntityKind.DATA_SET.name().equals(entityKindValueOrNull)
+ && permIdValueOrNull != null && permIdValueOrNull.contains(":");
+ }
+
+ /**
+ * Open the entity details tab for the specified entity kind and permId.
+ */
+ @Override
+ protected void openInitialEntityViewer(String entityKindValue, String permIdValue)
+ throws UserFailureException
+ {
+ EntityKind entityKind = getEntityKind(entityKindValue);
+ int idx = permIdValue.indexOf(':');
+
+ viewContext.getCommonService().getEntityInformationHolder(entityKind,
+ permIdValue.substring(0, idx),
+ new OpenEntityDetailsTabCallback(viewContext, permIdValue.substring(idx + 1)));
+ }
+
+ private static class OpenEntityDetailsTabCallback extends
+ AbstractAsyncCallback<IEntityInformationHolderWithPermId>
+ {
+ private final String wellLocation;
+
+ private OpenEntityDetailsTabCallback(final IViewContext<?> viewContext,
+ final String wellLocation)
+ {
+ super(viewContext);
+ this.wellLocation = wellLocation;
+ }
+
+ //
+ // AbstractAsyncCallback
+ //
+
+ /**
+ * Opens the tab with <var>result</var> entity details.
+ */
+ @Override
+ protected final void process(final IEntityInformationHolderWithPermId result)
+ {
+ new OpenEntityDetailsTabAction(new IEntityInformationHolderWithPermId()
+ {
+ private static final long serialVersionUID = 1L;
+
+ public BasicEntityType getEntityType()
+ {
+ return result.getEntityType();
+ }
+
+ public EntityKind getEntityKind()
+ {
+ return result.getEntityKind();
+ }
+
+ public Long getId()
+ {
+ return result.getId();
+ }
+
+ public String getCode()
+ {
+ return result.getCode();
+ }
+
+ public String getPermId()
+ {
+ return result.getPermId() + ":" + wellLocation;
+ }
+
+ }, viewContext, false).execute();
+ }
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java
index 03c5c3ec491..8ffbba35064 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java
@@ -97,8 +97,7 @@ public class PlateImageReference extends DatasetIdentifier
}
final PlateImageReference other = (PlateImageReference) obj;
- if ((channelOrNull == null && other.channelOrNull != null)
- || channelOrNull.equals(other.channelOrNull) == false)
+ if ((channelOrNull == null && other.channelOrNull != null) || channelOrNull.equals(other.channelOrNull) == false)
{
return false;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetEnrichedReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetEnrichedReference.java
index e8c84861080..d1bd2a8a2f9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetEnrichedReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetEnrichedReference.java
@@ -19,7 +19,9 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
import java.util.ArrayList;
import java.util.List;
-import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
@@ -28,7 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
* @author Tomasz Pylak
*/
// NOTE: is supposed to be extended with derived analysis datasets and optionally raw image datasets
-public class ImageDatasetEnrichedReference implements ISerializable
+public class ImageDatasetEnrichedReference implements IEntityInformationHolderWithPermId
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
@@ -69,4 +71,29 @@ public class ImageDatasetEnrichedReference implements ISerializable
{
return overlayDatasets;
}
+
+ public BasicEntityType getEntityType()
+ {
+ return imageDataset.getDatasetReference().getEntityType();
+ }
+
+ public EntityKind getEntityKind()
+ {
+ return imageDataset.getDatasetReference().getEntityKind();
+ }
+
+ public Long getId()
+ {
+ return imageDataset.getDatasetReference().getId();
+ }
+
+ public String getCode()
+ {
+ return imageDataset.getDatasetReference().getCode();
+ }
+
+ public String getPermId()
+ {
+ return imageDataset.getDatasetReference().getPermId();
+ }
}
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 4f6a1470137..4b6dc6f56dc 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
@@ -241,6 +241,16 @@ public class WellLocation implements ISerializable
return "(" + row + "," + column + ")";
}
+ public String toWellIdString()
+ {
+ return getNumberLetter(row) + column;
+ }
+
+ private String getNumberLetter(@SuppressWarnings("hiding") int row)
+ {
+ return Character.toString((char) ((char) row + 'A' - (char) 1));
+ }
+
@Override
public int hashCode()
{
--
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