From 171e68a86f54f2daf36d9aa511075dbea9d0948a Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 13 Jul 2009 11:14:53 +0000
Subject: [PATCH] LMS-1028 ProteinViewer showing properties
SVN: 11730
---
.../client/web/client/application/Dict.java | 5 ++
.../ProteinByExperimentBrowerToolBar.java | 5 ++
.../ProteinByExperimentBrowserGrid.java | 11 ++--
.../web/client/application/ProteinViewer.java | 57 ++++++++++++++-----
.../web/public/phosphonetx-dictionary.js | 4 ++
.../phosphonetx/server/PhosphoNetXServer.java | 1 +
.../server/dataaccess/IProteinQueryDAO.java | 2 +-
7 files changed, 64 insertions(+), 21 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
index e46fd56d9dd..f152a854585 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java
@@ -31,5 +31,10 @@ public class Dict
public static final String PROTEIN_DESCRIPTION = "protein_description";
public static final String FALSE_DISCOVERY_RATE = "false_discovery_rate";
public static final String DATA_SET = "data_set";
+
+ // Protein Viewer
+ public static final String PROTEIN_IN_EXPERIMENT_TAB_LABEL = "protein_in_experiment_tab_label";
+ public static final String EXPERIMENT_LABEL = "experiment_label";
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
index 235ebabbfc7..215b59c539a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
@@ -119,6 +119,11 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
});
add(new AdapterToolItem(fdrComboBox));
}
+
+ Experiment getExperimentOrNull()
+ {
+ return experiment;
+ }
void setBrowserGrid(ProteinByExperimentBrowserGrid browserGrid)
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
index 9be37d252a3..bd5591d5c67 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
@@ -56,23 +56,24 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+ private final ProteinByExperimentBrowerToolBar toolbar;
+
private ListProteinByExperimentCriteria criteria;
static IDisposableComponent create(
final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
- final ProteinByExperimentBrowerToolBar toolbar =
- new ProteinByExperimentBrowerToolBar(viewContext);
final ProteinByExperimentBrowserGrid browserGrid =
new ProteinByExperimentBrowserGrid(viewContext);
- toolbar.setBrowserGrid(browserGrid);
- return browserGrid.asDisposableWithToolbar(toolbar);
+ return browserGrid.asDisposableWithToolbar(browserGrid.toolbar);
}
private ProteinByExperimentBrowserGrid(final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, false);
specificViewContext = viewContext;
+ toolbar = new ProteinByExperimentBrowerToolBar(viewContext);
+ toolbar.setBrowserGrid(this);
setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID);
registerLinkClickListenerFor(ProteinColDefKind.DESCRIPTION.id(),
new ICellListener<ProteinInfo>()
@@ -80,7 +81,7 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
public void handle(ProteinInfo rowItem)
{
DispatcherHelper.dispatchNaviEvent(ProteinViewer.createTabItemFactory(
- viewContext, rowItem));
+ viewContext, toolbar.getExperimentOrNull(), rowItem));
}
});
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
index eb4afb12bde..3db1af446b4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
@@ -20,7 +20,11 @@ import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Set;
+import com.extjs.gxt.ui.client.Style.LayoutRegion;
+import com.extjs.gxt.ui.client.Style.Scroll;
import com.extjs.gxt.ui.client.widget.ContentPanel;
+import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
+import com.extjs.gxt.ui.client.widget.layout.BorderLayoutData;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
@@ -30,7 +34,11 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.IDatabaseModificationObserver;
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.ui.AbstractViewer;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.property.PropertyGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.StringUtils;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
@@ -42,7 +50,9 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExp
*
* @author Franz-Josef Elmer
*/
-public class ProteinViewer extends ContentPanel implements IDatabaseModificationObserver
+public class ProteinViewer extends
+ AbstractViewer<IPhosphoNetXClientServiceAsync, IEntityInformationHolder> implements
+ IDatabaseModificationObserver
{
private static final String PREFIX = "protein-viewer_";
@@ -50,7 +60,7 @@ public class ProteinViewer extends ContentPanel implements IDatabaseModification
static ITabItemFactory createTabItemFactory(
final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
- final ProteinInfo proteinInfo)
+ final Experiment experimentOrNull, final ProteinInfo proteinInfo)
{
return new ITabItemFactory()
{
@@ -62,11 +72,14 @@ public class ProteinViewer extends ContentPanel implements IDatabaseModification
public ITabItem create()
{
ProteinViewer viewer =
- new ProteinViewer(viewContext, proteinInfo.getExperimentID(),
- proteinInfo.getId());
+ new ProteinViewer(viewContext, experimentOrNull, proteinInfo.getId());
DatabaseModificationAwareComponent c =
new DatabaseModificationAwareComponent(viewer, viewer);
- return DefaultTabItem.create("Protein: " + proteinInfo.getDescription(), c,
+ String description = StringUtils.abbreviate(proteinInfo.getDescription(), 30);
+ String identifier =
+ experimentOrNull == null ? "?" : experimentOrNull.getIdentifier();
+ return DefaultTabItem.create(viewContext.getMessage(
+ Dict.PROTEIN_IN_EXPERIMENT_TAB_LABEL, description, identifier), c,
viewContext, false);
}
};
@@ -78,17 +91,17 @@ public class ProteinViewer extends ContentPanel implements IDatabaseModification
}
private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+ private final Experiment experimentOrNull;
private final TechId experimentID;
private final TechId proteinreferenceID;
- private final String widgetID;
- private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext, TechId experimentID,
- TechId proteinReferenceID)
+ private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ Experiment experimentOrNull, TechId proteinReferenceID)
{
- widgetID = createWidgetID(proteinReferenceID);
- setId(widgetID);
+ super(viewContext, "", createWidgetID(proteinReferenceID), false);
this.viewContext = viewContext;
- this.experimentID = experimentID;
+ this.experimentOrNull = experimentOrNull;
+ this.experimentID = TechId.create(experimentOrNull);
this.proteinreferenceID = proteinReferenceID;
reloadAllData();
}
@@ -101,11 +114,25 @@ public class ProteinViewer extends ContentPanel implements IDatabaseModification
private void recreateUI(ProteinByExperiment protein)
{
+ setLayout(new BorderLayout());
+ removeAll();
+ setScrollMode(Scroll.AUTO);
final Map<String, Object> properties = new LinkedHashMap<String, Object>();
- properties.put("Protein Description", protein.getDescription());
- properties.put("UniProt ID", protein.getUniprotID());
- final PropertyGrid propertyGrid = new PropertyGrid(viewContext, properties.size());
- add(propertyGrid);
+ if (experimentOrNull != null)
+ {
+ String identifier = experimentOrNull.getIdentifier();
+ properties.put(viewContext.getMessage(Dict.EXPERIMENT_LABEL), identifier);
+ }
+ properties.put(viewContext.getMessage(Dict.UNIPROT_ID), protein.getUniprotID());
+ properties.put(viewContext.getMessage(Dict.PROTEIN_DESCRIPTION), protein.getDescription());
+ PropertyGrid propertyGrid = new PropertyGrid(viewContext, properties.size());
+ propertyGrid.setProperties(properties);
+ ContentPanel contentPanel = new ContentPanel();
+ contentPanel.add(propertyGrid);
+ BorderLayoutData layoutData = createBorderLayoutData(LayoutRegion.WEST);
+ layoutData.setSize(400);
+ add(contentPanel, layoutData);
+ layout();
}
public DatabaseModificationKind[] getRelevantModifications()
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
index 2c16d381ae5..5ecb9cb5fdf 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js
@@ -11,6 +11,10 @@ var phosphonetx = {
protein_description: "Protein",
false_discovery_rate: "FDR",
+ // Protein in experiment viewer
+ protein_in_experiment_tab_label: "{0} in {1}",
+ experiment_label: "Experiment",
+
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
};
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index c580be21b74..68b5f87703b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -120,6 +120,7 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
proteinByExperiment.addSequence(proteinSequence);
}
+ sequences.close();
return proteinByExperiment;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
index 92ed67fc79c..4a1a8941582 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
@@ -38,7 +38,7 @@ public interface IProteinQueryDAO extends BaseQuery
@Select("select pr.id, pr.uniprot_id, pr.description, d.id as data_set_id, p.probability "
+ "from identified_proteins as ip left join proteins as p on ip.prot_id = p.id "
+ "left join data_sets as d on p.dase_id = d.id "
- + "left join experiments as e on d.expe_id = e.id, "
+ + "left join experiments as e on d.expe_id = e.id, "
+ "sequences as s left join protein_references as pr on s.prre_id = pr.id "
+ "where e.perm_id = ?{1} and ip.sequ_id = s.id order by pr.description")
public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(String experimentPermID);
--
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