From 831e2f27d207c25a49cf582a39d65296253985ff Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 10 May 2011 11:03:35 +0000
Subject: [PATCH] LMS-2190 gene and assay view polishing, small names
refactoring
SVN: 21192
---
.../FeatureVectorSummaryViewer.java | 45 +++---
.../detailviewers/LayoutUtils.java | 2 +
.../MaterialReplicaFeatureSummaryViewer.java | 134 +++++++++-------
.../detailviewers/PropertiesUtil.java | 148 ++++++++++++++++++
.../specific/ScreeningLinkExtractor.java | 2 +-
...MaterialReplicaFeatureSummaryProvider.java | 9 +-
.../MaterialFeatureVectorSummaryLoader.java | 82 +++++++---
.../logic/ReplicateSequenceProvider.java | 33 ++--
.../server/logic/WellContentLoader.java | 5 +-
.../MaterialAllReplicasFeatureVectors.java | 16 +-
.../dto/MaterialReplicaFeatureSummary.java | 5 +-
...aterialFeatureVectorSummaryLoaderTest.java | 2 +-
12 files changed, 345 insertions(+), 138 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PropertiesUtil.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/FeatureVectorSummaryViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/FeatureVectorSummaryViewer.java
index 270396fe9a2..11c2b5c103b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/FeatureVectorSummaryViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/FeatureVectorSummaryViewer.java
@@ -18,10 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.
import java.util.Set;
-import com.extjs.gxt.ui.client.Style.Orientation;
-import com.extjs.gxt.ui.client.util.Margins;
import com.extjs.gxt.ui.client.widget.Component;
-import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.layout.RowData;
import com.extjs.gxt.ui.client.widget.layout.RowLayout;
@@ -49,6 +46,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.u
*
* @author Kaloyan Enimanev
*/
+// TODO 2011-05-05, Tomasz Pylak: rename to ExperimentAnalysisSummaryViewer
public class FeatureVectorSummaryViewer
{
@@ -115,14 +113,14 @@ public class FeatureVectorSummaryViewer
@Override
public String tryGetLink()
{
- return ScreeningLinkExtractor.createFeatureVectorSummaryBrowserLink(experiment
- .getPermId());
+ return ScreeningLinkExtractor
+ .createExperimentAnalysisSummaryBrowserLink(experiment.getPermId());
}
@Override
public String getTabTitle()
{
- return "Feature Vector Summary: " + experiment.getCode();
+ return "Analysis Summary " + experiment.getCode();
}
@Override
@@ -139,14 +137,13 @@ public class FeatureVectorSummaryViewer
{
final LayoutContainer panel = new LayoutContainer();
- panel.setLayout(new RowLayout(Orientation.VERTICAL));
+ panel.setLayout(new RowLayout());
- Widget northPanel = createNorth(viewContext, experiment);
- panel.add(northPanel);
+ addHeader(panel, viewContext, experiment);
final IDisposableComponent gridComponent =
FeatureVectorSummaryGrid.create(viewContext, experiment);
- panel.add(gridComponent.getComponent());
+ panel.add(gridComponent.getComponent(), new RowData(-1, 1));
return new IDisposableComponent()
{
@@ -172,24 +169,26 @@ public class FeatureVectorSummaryViewer
};
}
- private static Widget createNorth(IViewContext<IScreeningClientServiceAsync> viewContext,
- Experiment experiment)
+ private static void addHeader(LayoutContainer parentPanel,
+ IViewContext<IScreeningClientServiceAsync> viewContext, Experiment experiment)
{
+ String headingText = "Assay " + experiment.getCode();
+
LayoutContainer panel = new LayoutContainer();
- panel.setLayout(new RowLayout(Orientation.VERTICAL));
+ panel.setLayout(new RowLayout());
- // NOTE: this should be refactored to an external CSS style
- String headingText = "Assay " + experiment.getCode();
- Html headingWidget = new Html(headingText);
- headingWidget.setTagName("h1");
- panel.add(headingWidget, new RowData(1, -1, headingTitleMargin()));
+ Widget headingWidget = PropertiesUtil.createHeaderTitle(headingText);
+ panel.add(headingWidget, PropertiesUtil.createHeaderTitleLayoutData());
- return panel;
- }
+ LayoutContainer propertiesPanel = new LayoutContainer();
+ propertiesPanel.setLayout(new RowLayout());
+ int propsHeight = PropertiesUtil.addProperties(experiment, propertiesPanel, null);
+ panel.add(propertiesPanel, new RowData(1, -1));
- private static Margins headingTitleMargin()
- {
- return new Margins(0, 0, 20, 0);
+ int headersHeight = 15;
+ int totalHeight = propsHeight + headersHeight;
+ parentPanel.add(panel,
+ new RowData(-1, totalHeight, PropertiesUtil.createHeaderInfoMargin()));
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LayoutUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LayoutUtils.java
index ba9e29158a7..25795762b8a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LayoutUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/LayoutUtils.java
@@ -26,6 +26,8 @@ import com.extjs.gxt.ui.client.widget.layout.RowData;
*/
public class LayoutUtils
{
+ public static final int ONE_HEADER_LINE_HEIGHT_PX = 15;
+
private static final int MARGIN_SIZE_PX = 10;
/** @return layout data with big margin on all sides */
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryViewer.java
index 5de170c288c..d22f5aab939 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaFeatureSummaryViewer.java
@@ -26,13 +26,12 @@ import java.util.Set;
import com.extjs.gxt.ui.client.Style.Orientation;
import com.extjs.gxt.ui.client.Style.Scroll;
-import com.extjs.gxt.ui.client.util.Margins;
import com.extjs.gxt.ui.client.widget.Component;
-import com.extjs.gxt.ui.client.widget.HorizontalPanel;
import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.Text;
import com.extjs.gxt.ui.client.widget.Viewport;
+import com.extjs.gxt.ui.client.widget.layout.ColumnLayout;
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.TableLayout;
@@ -54,7 +53,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.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;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
@@ -75,6 +73,14 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReplicaIma
*/
public class MaterialReplicaFeatureSummaryViewer
{
+ private static final String LOADING_IMAGES_DICT_MSG = "Loading images...";
+
+ private static final String REPLICATE_ABBREV_DICT_MSG = "repl.";
+
+ private static final String NO_IMAGES_AVAILABLE_DICT_MSG = "No images available.";
+
+ private static final String MATERIAL_ID_DICT_MSG = "Id";
+
private static final int ONE_IMAGE_SIZE_PX = 80;
public static void openTab(IViewContext<IScreeningClientServiceAsync> screeningViewContext,
@@ -88,7 +94,7 @@ public class MaterialReplicaFeatureSummaryViewer
private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
- public MaterialReplicaFeatureSummaryViewer(
+ private MaterialReplicaFeatureSummaryViewer(
IViewContext<IScreeningClientServiceAsync> screeningViewContext)
{
this.screeningViewContext = screeningViewContext;
@@ -118,7 +124,6 @@ public class MaterialReplicaFeatureSummaryViewer
screeningViewContext.getCommonService().getExperimentInfo(new TechId(experiment),
new AbstractAsyncCallback<Experiment>(screeningViewContext)
{
-
@Override
protected void process(Experiment result)
{
@@ -147,7 +152,6 @@ public class MaterialReplicaFeatureSummaryViewer
screeningViewContext.getService().getMaterialInfo(new TechId(material),
new AbstractAsyncCallback<Material>(screeningViewContext)
{
-
@Override
protected void process(Material result)
{
@@ -204,19 +208,20 @@ public class MaterialReplicaFeatureSummaryViewer
private class ImagesFoundCallback extends AbstractAsyncCallback<List<WellReplicaImage>>
{
- private final LayoutContainer panel;
+ private final LayoutContainer imagesPanel;
- ImagesFoundCallback(LayoutContainer panel)
+ ImagesFoundCallback(LayoutContainer imagesPanel)
{
super(screeningViewContext);
- this.panel = panel;
+ this.imagesPanel = imagesPanel;
}
@Override
protected void process(List<WellReplicaImage> images)
{
- panel.add(createImagePanel(images));
- panel.layout();
+ imagesPanel.removeAll();
+ imagesPanel.add(createImagePanel(images));
+ imagesPanel.layout();
}
}
@@ -224,7 +229,7 @@ public class MaterialReplicaFeatureSummaryViewer
{
if (images.isEmpty())
{
- return new Text("No images available.");
+ return new Text(NO_IMAGES_AVAILABLE_DICT_MSG);
}
String displayTypeId = ScreeningDisplayTypeIDGenerator.EXPERIMENT_CHANNEL.createID(null);
final IDefaultChannelState defaultChannelState =
@@ -245,15 +250,20 @@ public class MaterialReplicaFeatureSummaryViewer
labelToReplicasMap.remove(orphanGroupKey);
}
panel.add(createBiologicalReplicatesImagesPanel(labelToReplicasMap, channelChooser));
+ ensureAllImagesVisible(panel);
+ return panel;
+ }
+
+ // WORKAROUND: in normal mode the height of menu and tab is not taken into account,
+ // so we add empty space to make
+ private void ensureAllImagesVisible(LayoutContainer panel)
+ {
if (screeningViewContext.isSimpleOrEmbeddedMode() == false)
{
- // WORKAROUND: in normal mode the height of menu and tab is not taken into account,
- // so we add empty space to make
Text box = new Text();
box.setHeight(100);
panel.add(box);
}
- return panel;
}
private Widget createOrphanTechnicalReplicatesPanel(
@@ -333,7 +343,7 @@ public class MaterialReplicaFeatureSummaryViewer
private Widget createTechnicalReplicateLabel(int technicalReplicateSequence)
{
- return new Text("repl. " + technicalReplicateSequence);
+ return new Text(REPLICATE_ABBREV_DICT_MSG + " " + technicalReplicateSequence);
}
private Widget createEmptyBox()
@@ -413,8 +423,8 @@ public class MaterialReplicaFeatureSummaryViewer
panel.setLayout(new RowLayout(Orientation.VERTICAL));
panel.setScrollMode(Scroll.AUTOY);
- final Widget northPanel = createNorth(screeningViewContext, experiment, material);
- panel.add(northPanel);
+ Widget materialInfo = createMaterialInfo(screeningViewContext, experiment, material);
+ panel.add(materialInfo, new RowData(-1, -1, PropertiesUtil.createHeaderInfoMargin()));
final IDisposableComponent gridComponent =
MaterialReplicaFeatureSummaryGrid.create(screeningViewContext, new TechId(
@@ -422,8 +432,11 @@ public class MaterialReplicaFeatureSummaryViewer
// NOTE: if the width is 100% then the vertical scrollbar of the grid is not visible
panel.add(gridComponent.getComponent(), new RowData(0.97, 400));
+ LayoutContainer imagesPanel = new LayoutContainer();
+ imagesPanel.add(new Text(LOADING_IMAGES_DICT_MSG));
+ panel.add(imagesPanel);
screeningViewContext.getService().listWellImages(new TechId(material.getId()),
- new TechId(experiment.getId()), new ImagesFoundCallback(panel));
+ new TechId(experiment.getId()), new ImagesFoundCallback(imagesPanel));
return new IDisposableComponent()
{
@@ -449,43 +462,45 @@ public class MaterialReplicaFeatureSummaryViewer
};
}
- private static Widget createNorth(IViewContext<IScreeningClientServiceAsync> viewContext,
- Experiment experiment, Material material)
+ private static Widget createMaterialInfo(
+ final IViewContext<IScreeningClientServiceAsync> viewContext,
+ final Experiment experiment, final Material material)
{
- HorizontalPanel panel = new HorizontalPanel();
+ LayoutContainer panel = new LayoutContainer();
+ panel.setLayout(new RowLayout());
- Widget left = createNorthLeft(viewContext, experiment, material);
- panel.add(left);
+ Widget headerWidget = createHeaderWithLinks(viewContext, experiment, material);
+ panel.add(headerWidget, PropertiesUtil.createHeaderTitleLayoutData());
- Widget right = createNorthRight(viewContext, experiment, material);
- panel.add(right);
+ LayoutContainer materialPropertiesPanel = createMaterialPropertiesPanel(material);
+ panel.add(materialPropertiesPanel);
return panel;
}
- private static Widget createNorthLeft(
+ private static Widget createHeaderWithLinks(
final IViewContext<IScreeningClientServiceAsync> viewContext,
final Experiment experiment, final Material material)
{
- LayoutContainer panel = new LayoutContainer();
- panel.setLayout(new RowLayout(Orientation.VERTICAL));
+ Widget headingWidget = createHeaderTitle(experiment, material);
+ Text emptyBox = new Text();
+ emptyBox.setWidth(200);
+ Widget assayAnalysisSummaryLink =
+ createAssayAnalysisSummaryLink(viewContext, experiment, material);
+ LayoutContainer headerPanel = new LayoutContainer();
+ headerPanel.setLayout(new ColumnLayout());
+ headerPanel.add(headingWidget);
+ headerPanel.add(emptyBox);
+ headerPanel.add(assayAnalysisSummaryLink);
+ return headerPanel;
+ }
+ private static Html createHeaderTitle(final Experiment experiment, final Material material)
+ {
String headingText =
getMaterialType(material) + " " + getMaterialName(material) + " in assay "
+ experiment.getCode();
-
- Html headingWidget = createHeader(headingText);
- panel.add(headingWidget, new RowData(1, -1, new Margins(0, 0, 20, 0)));
-
- return panel;
- }
-
- private static Html createHeader(String headingText)
- {
- Html headingWidget = new Html(headingText);
- // NOTE: this should be refactored to an external CSS style
- headingWidget.setTagName("h1");
- return headingWidget;
+ return PropertiesUtil.createHeaderTitle(headingText);
}
private static String getMaterialType(Material material)
@@ -506,29 +521,24 @@ public class MaterialReplicaFeatureSummaryViewer
if (material.getEntityType().getCode()
.equalsIgnoreCase(ScreeningConstants.GENE_PLUGIN_TYPE_CODE))
{
- for (IEntityProperty property : material.getProperties())
+ String geneSymbol =
+ PropertiesUtil.tryFindProperty(material, ScreeningConstants.GENE_SYMBOLS);
+ if (geneSymbol != null)
{
- if (property.getPropertyType().getCode()
- .equalsIgnoreCase(ScreeningConstants.GENE_SYMBOLS))
- {
- return property.tryGetAsString();
- }
+ return geneSymbol;
}
}
return material.getCode();
}
- private static Widget createNorthRight(
+ private static Widget createAssayAnalysisSummaryLink(
final IViewContext<IScreeningClientServiceAsync> viewContext,
final Experiment experiment, final Material material)
{
- LayoutContainer panel = new LayoutContainer();
- panel.setLayout(new RowLayout(Orientation.VERTICAL));
-
// add link to feature vector summary for the experiment
String linkUrl =
- ScreeningLinkExtractor
- .createFeatureVectorSummaryBrowserLink(experiment.getPermId());
+ ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(experiment
+ .getPermId());
String linkText = "Show assay " + experiment.getCode() + " summary";
Widget linkWidget = LinkRenderer.getLinkWidget(linkText, new ClickHandler()
{
@@ -539,11 +549,17 @@ public class MaterialReplicaFeatureSummaryViewer
FeatureVectorSummaryViewer.openTab(viewContext, experiment.getPermId());
}
}, linkUrl);
+ return linkWidget;
+ }
- HorizontalPanel linkPanel = new HorizontalPanel();
- linkPanel.add(linkWidget);
- panel.add(linkPanel, new RowData(-1, -1, new Margins(0, 0, 20, 200)));
-
- return panel;
+ private static LayoutContainer createMaterialPropertiesPanel(final Material material)
+ {
+ LayoutContainer propertiesPanel = new LayoutContainer();
+ propertiesPanel.setLayout(new RowLayout());
+ Map<String, String> additionalProperties = new HashMap<String, String>();
+ additionalProperties.put(MATERIAL_ID_DICT_MSG, material.getCode());
+ PropertiesUtil.addProperties(material, propertiesPanel, additionalProperties,
+ ScreeningConstants.GENE_SYMBOLS);
+ return propertiesPanel;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PropertiesUtil.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PropertiesUtil.java
new file mode 100644
index 00000000000..37e4b9bbae0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PropertiesUtil.java
@@ -0,0 +1,148 @@
+/*
+ * 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.Arrays;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
+import com.extjs.gxt.ui.client.Style.HorizontalAlignment;
+import com.extjs.gxt.ui.client.Style.VerticalAlignment;
+import com.extjs.gxt.ui.client.util.Margins;
+import com.extjs.gxt.ui.client.widget.Html;
+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.TableData;
+import com.extjs.gxt.ui.client.widget.layout.TableLayout;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.lang.StringEscapeUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithProperties;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+
+/**
+ * Utility methods to display properties and header in the publication views.
+ *
+ * @author Tomasz Pylak
+ */
+public class PropertiesUtil
+{
+ public static String tryFindProperty(IEntityPropertiesHolder propertiesHolder,
+ String propertyCode)
+ {
+ for (IEntityProperty property : propertiesHolder.getProperties())
+ {
+ if (property.getPropertyType().getCode().equalsIgnoreCase(propertyCode))
+ {
+ return property.tryGetAsString();
+ }
+ }
+ return null;
+ }
+
+ /** @return estimated height */
+ public static int addProperties(IEntityInformationHolderWithProperties propertiesHolder,
+ LayoutContainer panel,
+ Map<String/* label */, String/* value */> additionalPropertiesOrNull,
+ String... excludedPropertyCodes)
+ {
+ LayoutContainer propertiesPanel = new LayoutContainer();
+ propertiesPanel.setLayout(new TableLayout(3));
+
+ Map<String, String> propertiesMap =
+ createSortedMap(propertiesHolder, excludedPropertyCodes, additionalPropertiesOrNull);
+ int height = 0;
+ for (Entry<String, String> entry : propertiesMap.entrySet())
+ {
+ addProperty(propertiesPanel, entry.getKey(), entry.getValue());
+ height += getEstimatedHeight(entry.getValue());
+ }
+ panel.add(propertiesPanel);
+ return height;
+ }
+
+ private static Map<String, String> createSortedMap(
+ IEntityInformationHolderWithProperties propertiesHolder,
+ String[] excludedPropertyCodes, Map<String, String> additionalPropertiesOrNull)
+ {
+ Set<String> excludedPropertyCodesSet =
+ new HashSet<String>(Arrays.asList(excludedPropertyCodes));
+
+ Map<String, String> propertiesMap = new TreeMap<String, String>();
+ for (IEntityProperty property : propertiesHolder.getProperties())
+ {
+ PropertyType propertyType = property.getPropertyType();
+ if (excludedPropertyCodesSet.contains(propertyType.getCode()) == false)
+ {
+ String value = property.tryGetAsString();
+ if (value != null && value.length() > 0)
+ {
+ propertiesMap.put(propertyType.getLabel(), value);
+ }
+ }
+ }
+ if (additionalPropertiesOrNull != null)
+ {
+ for (Entry<String, String> entry : additionalPropertiesOrNull.entrySet())
+ {
+ propertiesMap.put(entry.getKey(), entry.getValue());
+ }
+ }
+ return propertiesMap;
+ }
+
+ private static void addProperty(LayoutContainer propertiesPanel, String label, String value)
+ {
+ TableData labelLayout = new TableData(HorizontalAlignment.RIGHT, VerticalAlignment.TOP);
+ labelLayout.setWidth("80px");
+ propertiesPanel.add(new Html(label + ": "), labelLayout);
+ TableData spacerLayout = new TableData();
+ spacerLayout.setWidth("5px");
+ propertiesPanel.add(new Text(""), spacerLayout);
+ TableData valueLayout = new TableData(HorizontalAlignment.LEFT, VerticalAlignment.TOP);
+ propertiesPanel.add(new Html(StringEscapeUtils.unescapeHtml(value)), valueLayout);
+ }
+
+ private static int getEstimatedHeight(String text)
+ {
+ int charsPerLine = 150;
+ return LayoutUtils.ONE_HEADER_LINE_HEIGHT_PX * ((text.length() / charsPerLine) + 1);
+ }
+
+ public static Margins createHeaderInfoMargin()
+ {
+ return new Margins(3, 3, 10, 3);
+ }
+
+ public static RowData createHeaderTitleLayoutData()
+ {
+ return new RowData(-1, -1, new Margins(0, 0, 5, 0));
+ }
+
+ public static Html createHeaderTitle(String headingText)
+ {
+ Html headingWidget = new Html(headingText);
+ // NOTE: this should be refactored to an external CSS style
+ headingWidget.setTagName("h1");
+ return headingWidget;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
index fad783068ca..264b99992b7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
@@ -88,7 +88,7 @@ public class ScreeningLinkExtractor extends LinkExtractor
return tryPrint(url);
}
- public static final String createFeatureVectorSummaryBrowserLink(String experimentPermId)
+ public static final String createExperimentAnalysisSummaryBrowserLink(String experimentPermId)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER, FEATURE_VECTOR_SUMMARY_ACTION);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java
index e8a3324832c..bcd8e51afe5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/MaterialReplicaFeatureSummaryProvider.java
@@ -88,7 +88,7 @@ class MaterialReplicaFeatureSummaryProvider extends
builder.columnGroup(subgroup);
}
- if (rows.get(0).getTechnicalReplicates() != null)
+ if (rows.get(0).getDirectTechnicalReplicates() != null)
{
builder.columnGroup(DEFAULT_SUBGROUP);
}
@@ -111,7 +111,8 @@ class MaterialReplicaFeatureSummaryProvider extends
builder.column(DEVIATION).addDouble(row.getFeatureVectorDeviation());
builder.column(RANK).addInteger((long) row.getFeatureVectorRank());
- MaterialBiologicalReplicateFeatureSummary defaultSubgroup = row.getTechnicalReplicates();
+ MaterialBiologicalReplicateFeatureSummary defaultSubgroup =
+ row.getDirectTechnicalReplicates();
if (defaultSubgroup != null)
{
addSubgroup(builder, DEFAULT_SUBGROUP, "", defaultSubgroup);
@@ -141,7 +142,9 @@ class MaterialReplicaFeatureSummaryProvider extends
.withTitle(replicaColumnTitle).addDouble((double) featureValues[i]);
}
- if (false == DEFAULT_SUBGROUP.equals(groupId))
+ // aggregates should be shown only for biological replicates which have more than one
+ // technical replicate
+ if (false == DEFAULT_SUBGROUP.equals(groupId) && featureValues.length > 1)
{
MaterialReplicaSummaryAggregationType aggregationType =
subgroup.getSummaryAggregationType();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
index ccc887bbf1f..672cee58449 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.Comparator;
import java.util.List;
import ch.rinn.restrictions.Private;
@@ -77,8 +78,6 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
{
return replicaRows;
}
- final List<MaterialBiologicalReplicateFeatureVector> backendSubgroups =
- backendResult.getSubgroups();
float[] featureVectorDeviatons =
backendResult.getGeneralSummary().getFeatureVectorDeviations();
@@ -99,18 +98,20 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
replicaRow.setFeatureVectorRank(featureVectorRanks[i]);
replicaRow.setFeatureDescription(featureDescriptions.get(i));
- float[] defaultFeatureValues = extractFeatureValues(i, backendResult.getReplicas());
+ float[] defaultFeatureValues =
+ extractFeatureValues(i, backendResult.getDirectTechnicalReplicates());
if (defaultFeatureValues != null)
{
MaterialBiologicalReplicateFeatureSummary defaultReplica =
new MaterialBiologicalReplicateFeatureSummary(defaultFeatureValues, 0,
MaterialReplicaSummaryAggregationType.MEDIAN);
- replicaRow.setTechnicalReplicates(defaultReplica);
+ replicaRow.setDirectTechnicalReplicates(defaultReplica);
}
+ final List<MaterialBiologicalReplicateFeatureVector> backendSubgroups =
+ backendResult.getBiologicalReplicates();
List<MaterialBiologicalReplicateFeatureSummary> subgroups =
new ArrayList<MaterialBiologicalReplicateFeatureSummary>();
- replicaRow.setBiologicalRelicates(subgroups);
for (int tmp = 0; tmp < backendSubgroups.size(); tmp++)
{
MaterialBiologicalReplicateFeatureVector backendGroup = backendSubgroups.get(tmp);
@@ -122,6 +123,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
aggregatedSummaries[i], backendGroup.getSummaryAggregationType());
subgroups.add(subgroup);
}
+ replicaRow.setBiologicalRelicates(subgroups);
}
return replicaRows;
}
@@ -135,7 +137,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
return subgroupLabels;
}
for (MaterialBiologicalReplicateFeatureVector backendSubgroup : backendResultOrNull
- .getSubgroups())
+ .getBiologicalReplicates())
{
subgroupLabels.add(backendSubgroup.getSubgroupLabel());
}
@@ -148,8 +150,8 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
float[] result = new float[replicas.size()];
for (int pos = 0; pos < result.length; pos++)
{
- float[] aggregatedValues = replicas.get(pos).getFeatueVector();
- result[pos] = aggregatedValues[i];
+ float[] featureVector = replicas.get(pos).getFeatueVector();
+ result[pos] = featureVector[i];
}
return result;
}
@@ -191,15 +193,11 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
new ReplicateSequenceProvider(materialWells,
settings.getBiologicalReplicatePropertyTypeCodes());
- List<MaterialBiologicalReplicateFeatureVector> subgroups = Collections.emptyList();
- List<MaterialTechnicalReplicateFeatureVector> replicas = Collections.emptyList();
- if (replicaSequences.hasNoBiologicalReplicates())
- {
- replicas = createTechnicalReplicas(materialWells, replicaSequences);
- } else
- {
- subgroups = createBiologicalReplicates(materialWells, replicaSequences);
- }
+ List<MaterialBiologicalReplicateFeatureVector> subgroups =
+ createBiologicalReplicates(materialWells, replicaSequences);
+ List<MaterialTechnicalReplicateFeatureVector> replicas =
+ filterDirectTechnicalReplicas(materialWells, replicaSequences);
+
return new MaterialAllReplicasFeatureVectors(experimentWells.getFeatureDescriptions(),
materialGeneralSummary, subgroups, replicas);
}
@@ -213,7 +211,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
List<MaterialBiologicalReplicateFeatureVector> subgroups =
new ArrayList<MaterialBiologicalReplicateFeatureVector>();
MaterialReplicaSummaryAggregationType aggregationType = settings.getAggregationType();
- for (Integer biologicalReplicateSeq : replicaSequences.getBiologicalReplicateKeys())
+ for (Integer biologicalReplicateSeq : replicaSequences.getBiologicalReplicateSequences())
{
List<IWellData> technicalReplicateWells =
biologicalReplicateMap.getOrDie(biologicalReplicateSeq);
@@ -233,7 +231,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
WellReplicaSummaryCalculator.calculateSummaryFeatureVector(technicalReplicateWells,
aggregationType);
List<MaterialTechnicalReplicateFeatureVector> replicas =
- createTechnicalReplicas(technicalReplicateWells, replicaSequences);
+ createTechnicalReplicates(technicalReplicateWells, replicaSequences);
String subgroupLabel = getSubgroupLabel(technicalReplicateWells, replicaSequences);
return new MaterialBiologicalReplicateFeatureVector(replicas, aggregatedSummary,
aggregationType, subgroupLabel);
@@ -246,7 +244,9 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
// all wells belong to the same subgroup, so it does not matter which one we take
Sample well = subgroupWellDataList.get(0).getWell();
- return replicaSequences.getBiologicalReplicateLabel(well);
+ String label = replicaSequences.tryGetBiologicalReplicateLabel(well);
+ assert label != null : "no biological replicates!";
+ return label;
}
private MaterialFeatureVectorSummary tryCalculateMaterialSummary(TechId materialId,
@@ -257,14 +257,30 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
return tryFindMaterialSummary(materialId, featureSummaries);
}
- private static List<MaterialTechnicalReplicateFeatureVector> createTechnicalReplicas(
- List<IWellData> materialWellDataList, ReplicateSequenceProvider replicaSequences)
+ // chooses wells which have no information about which biological replicate they are
+ private static List<MaterialTechnicalReplicateFeatureVector> filterDirectTechnicalReplicas(
+ List<IWellData> materialWellDataList, final ReplicateSequenceProvider replicaSequences)
+ {
+ List<IWellData> directTechnicalReplicas =
+ CollectionUtils.filter(materialWellDataList, new ICollectionFilter<IWellData>()
+ {
+ public boolean isPresent(IWellData element)
+ {
+ return replicaSequences.isBiologicalReplicate(element) == false;
+ }
+ });
+ sortByTechnicalReplicateSequence(directTechnicalReplicas, replicaSequences);
+ return createTechnicalReplicates(directTechnicalReplicas, replicaSequences);
+ }
+
+ private static List<MaterialTechnicalReplicateFeatureVector> createTechnicalReplicates(
+ List<IWellData> wells, final ReplicateSequenceProvider replicaSequences)
{
List<MaterialTechnicalReplicateFeatureVector> replicas =
new ArrayList<MaterialTechnicalReplicateFeatureVector>();
- for (IWellData wellData : materialWellDataList)
+ for (IWellData wellData : wells)
{
- int replicaSequenceNumber = replicaSequences.getTechnicalReplicateSequenceNum(wellData);
+ int replicaSequenceNumber = replicaSequences.getTechnicalReplicateSequence(wellData);
MaterialTechnicalReplicateFeatureVector featureVector =
new MaterialTechnicalReplicateFeatureVector(replicaSequenceNumber,
wellData.getFeatureVector());
@@ -273,6 +289,22 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
return replicas;
}
+ private static void sortByTechnicalReplicateSequence(List<IWellData> materialWellDataList,
+ final ReplicateSequenceProvider replicaSequences)
+ {
+ Collections.sort(materialWellDataList, new Comparator<IWellData>()
+ {
+ public int compare(IWellData w1, IWellData w2)
+ {
+ Integer replicaSequenceNumber1 =
+ replicaSequences.getTechnicalReplicateSequence(w1);
+ Integer replicaSequenceNumber2 =
+ replicaSequences.getTechnicalReplicateSequence(w2);
+ return replicaSequenceNumber1.compareTo(replicaSequenceNumber2);
+ }
+ });
+ }
+
private static List<IWellData> filterWellsByMaterial(List<IWellData> wellDataList,
final TechId materialId)
{
@@ -295,7 +327,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
{
public Integer getKey(IWellData wellData)
{
- return replicaSequences.tryGetBiologicalReplicateSequenceNum(wellData.getWell());
+ return replicaSequences.tryGetBiologicalReplicateSequence(wellData.getWell());
}
});
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ReplicateSequenceProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ReplicateSequenceProvider.java
index ba11ffca355..69d334ba5c0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ReplicateSequenceProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ReplicateSequenceProvider.java
@@ -22,7 +22,6 @@ import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import ch.systemsx.cisd.common.collections.GroupByMap;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
@@ -46,14 +45,15 @@ class ReplicateSequenceProvider
public ReplicateSequenceProvider(List<? extends IEntityPropertiesHolder> replicaWells,
List<String> biologicalReplicatePropertyTypeCodesOrNull)
{
- this.biologicalReplicatePropertyTypeCodesOrNull = biologicalReplicatePropertyTypeCodesOrNull;
+ this.biologicalReplicatePropertyTypeCodesOrNull =
+ biologicalReplicatePropertyTypeCodesOrNull;
this.biologicalReplicateSeqMap = new LinkedHashMap<Double, Integer>();
this.technicalReplicateSeqMap = new LinkedHashMap<Long, Integer>();
GroupByMap<Double, IEntityPropertiesHolder> biologicalReplicates =
groupByBiologicalReplicate(replicaWells);
int biologicalReplicateSeq = 1;
- for (Double biologicalReplicateKey : createSortedCopy(biologicalReplicates.getKeys()))
+ for (Double biologicalReplicateKey : biologicalReplicates.getKeys())
{
if (biologicalReplicateKey != null)
{
@@ -70,7 +70,8 @@ class ReplicateSequenceProvider
}
}
- public Collection<Integer> getBiologicalReplicateKeys()
+ /** @return sequences of biological replicas, all keys are not null. */
+ public Collection<Integer> getBiologicalReplicateSequences()
{
return createSortedCopy(biologicalReplicateSeqMap.values());
}
@@ -87,8 +88,14 @@ class ReplicateSequenceProvider
});
}
+ /** @return true if this well has information about which biological replicate it is. */
+ public boolean isBiologicalReplicate(IEntityPropertiesHolder well)
+ {
+ return tryFindSubgroup(well) != null;
+ }
+
/** Subgroup sequence, the same for all technical replicates of one biological replicate. */
- public Integer tryGetBiologicalReplicateSequenceNum(IEntityPropertiesHolder well)
+ public Integer tryGetBiologicalReplicateSequence(IEntityPropertiesHolder well)
{
Double subgroupKey = tryFindSubgroup(well);
if (subgroupKey == null)
@@ -103,7 +110,7 @@ class ReplicateSequenceProvider
/**
* Technical Replicate Sequence (unique in one biological replicate)
*/
- public int getTechnicalReplicateSequenceNum(IEntityPropertiesHolder well)
+ public int getTechnicalReplicateSequence(IEntityPropertiesHolder well)
{
return technicalReplicateSeqMap.get(well.getId());
}
@@ -115,15 +122,13 @@ class ReplicateSequenceProvider
return sortedKeys;
}
- public boolean hasNoBiologicalReplicates()
+ public String tryGetBiologicalReplicateLabel(IEntityPropertiesHolder well)
{
- Set<Double> keys = biologicalReplicateSeqMap.keySet();
- return keys.size() == 1 && keys.contains(null);
- }
-
- public String getBiologicalReplicateLabel(IEntityPropertiesHolder well)
- {
- int biologicalReplicateSeq = tryGetBiologicalReplicateSequenceNum(well);
+ Integer biologicalReplicateSeq = tryGetBiologicalReplicateSequence(well);
+ if (biologicalReplicateSeq == null)
+ {
+ return null;
+ }
IEntityProperty subgroupProperty = tryFindSubgroupProperty(well);
assert subgroupProperty != null : "cannot fnd the subgroup property";
boolean isMaterialProperty = (subgroupProperty.getMaterial() != null);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
index 99757e5a419..49a4459d5ff 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
@@ -169,8 +169,9 @@ public class WellContentLoader extends AbstractContentLoader
ReplicateSequenceProvider replicaSequences)
{
int technicalReplicaSequenceNumber =
- replicaSequences.getTechnicalReplicateSequenceNum(wellContent);
- String biologicalReplicateLabel = replicaSequences.getBiologicalReplicateLabel(wellContent);
+ replicaSequences.getTechnicalReplicateSequence(wellContent);
+ String biologicalReplicateLabel =
+ replicaSequences.tryGetBiologicalReplicateLabel(wellContent);
return new WellReplicaImage(wellContent, technicalReplicaSequenceNumber,
biologicalReplicateLabel);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialAllReplicasFeatureVectors.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialAllReplicasFeatureVectors.java
index 658782483fb..c509cde17e6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialAllReplicasFeatureVectors.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/MaterialAllReplicasFeatureVectors.java
@@ -22,10 +22,10 @@ public class MaterialAllReplicasFeatureVectors implements ISerializable
private MaterialFeatureVectorSummary generalSummary;
// NOTE: Can be empty.
- private List<MaterialBiologicalReplicateFeatureVector> subgroups;
+ private List<MaterialBiologicalReplicateFeatureVector> biologicalReplicates;
// NOTE: Can be empty. Used for replicas which have no subgroups
- private List<MaterialTechnicalReplicateFeatureVector> replicas;
+ private List<MaterialTechnicalReplicateFeatureVector> directTechnicalReplicates;
// GWT only
@SuppressWarnings("unused")
@@ -40,8 +40,8 @@ public class MaterialAllReplicasFeatureVectors implements ISerializable
{
this.featureDescriptions = featureDescriptions;
this.generalSummary = generalSummary;
- this.subgroups = subgroups;
- this.replicas = replicas;
+ this.biologicalReplicates = subgroups;
+ this.directTechnicalReplicates = replicas;
}
public List<CodeAndLabel> getFeatureDescriptions()
@@ -54,14 +54,14 @@ public class MaterialAllReplicasFeatureVectors implements ISerializable
return generalSummary;
}
- public List<MaterialBiologicalReplicateFeatureVector> getSubgroups()
+ public List<MaterialBiologicalReplicateFeatureVector> getBiologicalReplicates()
{
- return subgroups;
+ return biologicalReplicates;
}
- public List<MaterialTechnicalReplicateFeatureVector> getReplicas()
+ public List<MaterialTechnicalReplicateFeatureVector> getDirectTechnicalReplicates()
{
- return replicas;
+ return directTechnicalReplicates;
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummary.java
index eb94e95da5d..a5e5d35e584 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialReplicaFeatureSummary.java
@@ -96,12 +96,13 @@ public class MaterialReplicaFeatureSummary implements ISerializable
this.biologicalRelicates = replicaSubgroups;
}
- public MaterialBiologicalReplicateFeatureSummary getTechnicalReplicates()
+ public MaterialBiologicalReplicateFeatureSummary getDirectTechnicalReplicates()
{
return technicalReplicates;
}
- public void setTechnicalReplicates(MaterialBiologicalReplicateFeatureSummary defaultReplica)
+ public void setDirectTechnicalReplicates(
+ MaterialBiologicalReplicateFeatureSummary defaultReplica)
{
this.technicalReplicates = defaultReplica;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
index f966bad4db2..d347bdeac9d 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
@@ -95,7 +95,7 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
assertEquals(featuresDesc, featureVectors.getFeatureDescriptions());
int groupId = 1;
- for (MaterialBiologicalReplicateFeatureVector subgroup : featureVectors.getSubgroups())
+ for (MaterialBiologicalReplicateFeatureVector subgroup : featureVectors.getBiologicalReplicates())
{
switch (groupId)
{
--
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