From 5e8558bfd07649bb02288667ba29bcd52698fa1d Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 15 Mar 2011 13:18:19 +0000
Subject: [PATCH] LMS-2103 Wizard framework slightly modified.
BiologicalSampleCreatingPage implemented.
SVN: 20332
---
.../DatabaseModificationAwareObject.java | 5 +
.../application/framework/DefaultTabItem.java | 8 +-
.../ui/sample/SampleTypeSelectionWidget.java | 11 +-
.../search/DetailedSearchCriterionWidget.java | 3 +
.../client/application/ui/wizard/Wizard.java | 32 ++++-
.../application/ui/wizard/WizardPage.java | 14 ++
.../shared/basic/dto/DetailedSearchField.java | 5 +-
...AbstractGenericSampleRegisterEditForm.java | 11 +-
.../web/client/IPhosphoNetXClientService.java | 4 +
.../IPhosphoNetXClientServiceAsync.java | 5 +
.../client/application/PhosphoNetXModule.java | 2 +-
.../wizard/BiologicalSampleChoosingPage.java | 5 +-
.../wizard/BiologicalSampleCreatingPage.java | 130 +++++++++++++++++-
.../MsInjectionSampleAnnotationModel.java | 38 +++--
.../MsInjectionSampleAnnotationWizard.java | 2 +-
.../wizard/MsInjectionSampleChoosingPage.java | 14 +-
.../application/wizard/QuestionPage.java | 10 +-
.../web/public/phosphonetx-dictionary.js | 16 +++
.../web/server/PhosphoNetXClientService.java | 17 ++-
.../resultset/BiologicalSampleProvider.java | 2 +-
.../ParentlessMsInjectionSampleProvider.java | 3 +-
21 files changed, 287 insertions(+), 50 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DatabaseModificationAwareObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DatabaseModificationAwareObject.java
index 4977e764054..05f32deef80 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DatabaseModificationAwareObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DatabaseModificationAwareObject.java
@@ -66,6 +66,11 @@ public class DatabaseModificationAwareObject<T> implements IDatabaseModification
this.modificationObserver = modificationObserver;
}
+ public IDatabaseModificationObserver getModificationObserver()
+ {
+ return modificationObserver;
+ }
+
public DatabaseModificationKind[] getRelevantModifications()
{
return modificationObserver.getRelevantModifications();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DefaultTabItem.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DefaultTabItem.java
index b78e92ed8a2..48fc3802cf8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DefaultTabItem.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/framework/DefaultTabItem.java
@@ -81,7 +81,13 @@ public class DefaultTabItem implements ITabItem
final DatabaseModificationAwareComponent component, IViewContext<?> viewContext,
boolean isCloseConfirmationNeeded)
{
- return create(viewContext, title, component.get(), component, null,
+ IDelegatedAction disposer = null;
+ IDatabaseModificationObserver modificationObserver = component.getModificationObserver();
+ if (modificationObserver instanceof IDisposableComponent)
+ {
+ disposer = createDisposer((IDisposableComponent) modificationObserver);
+ }
+ return create(viewContext, title, component.get(), component, disposer,
isCloseConfirmationNeeded);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleTypeSelectionWidget.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleTypeSelectionWidget.java
index b0116a10313..71c5d1abebc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleTypeSelectionWidget.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/sample/SampleTypeSelectionWidget.java
@@ -43,7 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
*
* @author Izabela Adamczyk
*/
-public final class SampleTypeSelectionWidget extends DropDownList<SampleTypeModel, SampleType>
+public class SampleTypeSelectionWidget extends DropDownList<SampleTypeModel, SampleType>
{
public static final String SUFFIX = "sample-type";
@@ -138,6 +138,14 @@ public final class SampleTypeSelectionWidget extends DropDownList<SampleTypeMode
edit(ObjectKind.PROPERTY_TYPE_ASSIGNMENT) };
}
+ /**
+ * Filters sample types returned from server. This is a hook method which does nothing. Can be
+ * overridden by subclasses.
+ */
+ protected void filterTypes(List<SampleType> types)
+ {
+ }
+
//
// initial value support
//
@@ -163,6 +171,7 @@ public final class SampleTypeSelectionWidget extends DropDownList<SampleTypeMode
@Override
public void process(List<SampleType> result)
{
+ filterTypes(result);
super.process(result);
selectInitialValue();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/search/DetailedSearchCriterionWidget.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/search/DetailedSearchCriterionWidget.java
index 6a942bdf37b..32d128cd6f2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/search/DetailedSearchCriterionWidget.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/search/DetailedSearchCriterionWidget.java
@@ -254,6 +254,9 @@ public class DetailedSearchCriterionWidget extends HorizontalPanel
case ANY_PROPERTY:
description = "Any Property";
break;
+ case REGISTRATOR:
+ description = "";
+ break;
}
DetailedSearchFieldComboModel model = new DetailedSearchFieldComboModel(description, field);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/Wizard.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/Wizard.java
index b77b997516b..6044d99e1e9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/Wizard.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/Wizard.java
@@ -21,18 +21,22 @@ import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import com.extjs.gxt.ui.client.widget.Component;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.MessageBox;
import com.extjs.gxt.ui.client.widget.TabItem;
import com.extjs.gxt.ui.client.widget.layout.CardLayout;
import com.google.gwt.user.client.ui.Widget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+
/**
* Container of {@link WizardPage} instance. Manages changing between pages.
*
* @author Franz-Josef Elmer
*/
-public class Wizard<M extends IWizardDataModel> extends LayoutContainer
+public class Wizard<M extends IWizardDataModel> extends LayoutContainer implements IDisposableComponent
{
private final CardLayout layout;
@@ -86,6 +90,28 @@ public class Wizard<M extends IWizardDataModel> extends LayoutContainer
workflowModel.nextState();
}
+ public void update(Set<DatabaseModificationKind> observedModifications)
+ {
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[0];
+ }
+
+ public Component getComponent()
+ {
+ return this;
+ }
+
+ public void dispose()
+ {
+ for (WizardPage<M> page : visitedPages)
+ {
+ page.destroy();
+ }
+ }
+
private void changePage(IWizardState previousStateOrNull, IWizardState currentStateOrNull)
{
if (currentStateOrNull != null)
@@ -106,10 +132,6 @@ public class Wizard<M extends IWizardDataModel> extends LayoutContainer
{
String message = model.finish();
MessageBox.info("Info", message, null);
- for (WizardPage<M> page : visitedPages)
- {
- page.destroy();
- }
Widget parent = getParent();
if (parent instanceof TabItem)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardPage.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardPage.java
index 07a175e3ecc..fd257fd6caa 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardPage.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardPage.java
@@ -22,6 +22,7 @@ import com.extjs.gxt.ui.client.event.SelectionListener;
import com.extjs.gxt.ui.client.util.Margins;
import com.extjs.gxt.ui.client.widget.Component;
import com.extjs.gxt.ui.client.widget.ContentPanel;
+import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.extjs.gxt.ui.client.widget.button.Button;
import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
@@ -40,10 +41,12 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMess
*/
public class WizardPage<M extends IWizardDataModel> extends LayoutContainer
{
+ private static final String _LEFT_CONTENT = "_left_content";
public static final String PREVIOUS_BUTTON_LABEL_KEY = "wizard_page_previous_button_label";
public static final String NEXT_BUTTON_LABEL_KEY = "wizard_page_next_button_label";
public static final String FINISH_BUTTON_LABEL_KEY = "wizard_page_finish_button_label";
+ private final IMessageProvider messageProvider;
protected final M model;
private final IWizardState state;
private final LayoutContainer leftContent;
@@ -60,6 +63,7 @@ public class WizardPage<M extends IWizardDataModel> extends LayoutContainer
public WizardPage(IMessageProvider messageProvider, IWizardState state, final M model)
{
super(new BorderLayout());
+ this.messageProvider = messageProvider;
this.state = state;
this.model = model;
LayoutContainer leftCenterPanel = new LayoutContainer(new CenterLayout());
@@ -110,6 +114,16 @@ public class WizardPage<M extends IWizardDataModel> extends LayoutContainer
return state;
}
+ /**
+ * Sets the content of the left panel by an HTML snippet defined in the dictionary by the
+ * specified key. Note that the complete key in the dictionary reads <code><wizard
+ * state>_left_content</code>.
+ */
+ public void setLeftContentByDictionary()
+ {
+ setLeftContentBy(new Html(messageProvider.getMessage(state + _LEFT_CONTENT)));
+ }
+
/**
* Sets the content of the left hand part of this wizard page.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java
index 4c17e28826b..de671983559 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/DetailedSearchField.java
@@ -64,10 +64,9 @@ public class DetailedSearchField implements ISerializable
return createAttributeField(attributeFieldKind.getCode());
}
- public static DetailedSearchField createRegistratorField(
- String userID)
+ public static DetailedSearchField createRegistratorField()
{
- return new DetailedSearchField(DetailedSearchFieldKind.REGISTRATOR, userID);
+ return new DetailedSearchField(DetailedSearchFieldKind.REGISTRATOR, null);
}
private static DetailedSearchField createAttributeField(String code)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java
index 1fc05d62b78..5b40674ad19 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java
@@ -25,6 +25,7 @@ import com.extjs.gxt.ui.client.event.ButtonEvent;
import com.extjs.gxt.ui.client.event.Events;
import com.extjs.gxt.ui.client.event.SelectionListener;
import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.form.Field;
import com.extjs.gxt.ui.client.widget.form.FormPanel;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
@@ -340,7 +341,13 @@ abstract public class AbstractGenericSampleRegisterEditForm extends
protected final String createSampleIdentifier()
{
- final Space space = groupSelectionWidget.tryGetSelectedSpace();
+ return createSampleIdentifier(groupSelectionWidget, codeField);
+ }
+
+ public static final String createSampleIdentifier(SpaceSelectionWidget spaceSelectionWidget,
+ Field<String> codeField)
+ {
+ final Space space = spaceSelectionWidget.tryGetSelectedSpace();
final boolean shared = SpaceSelectionWidget.isSharedSpace(space);
final String code = codeField.getValue();
final StringBuilder builder = new StringBuilder("/");
@@ -351,7 +358,7 @@ abstract public class AbstractGenericSampleRegisterEditForm extends
builder.append(code);
return builder.toString().toUpperCase();
}
-
+
/** sets visibility of container and parent fields dependent on sample type */
private final void setContainerAndParentVisibility(final SampleType sampleType)
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
index 2dbdbfe6c6f..a299c9d8cc1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
@@ -64,6 +65,9 @@ public interface IPhosphoNetXClientService extends IClientService
public void linkSamples(Sample parentSample, List<Sample> childSamples) throws UserFailureException;
+ public void createAndLinkSamples(NewSample newBiologicalSample,
+ List<Sample> msInjectionSamples) throws UserFailureException;
+
public Vocabulary getTreatmentTypeVocabulary() throws UserFailureException;
public List<AbundanceColumnDefinition> getAbundanceColumnDefinitionsForProteinByExperiment(
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
index baa9472aebc..84e9b6986a1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
@@ -61,6 +62,10 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
/** @see IPhosphoNetXClientService#linkSamples(Sample, List) */
public void linkSamples(Sample parentSample, List<Sample> childSamples, AsyncCallback<Void> callback);
+ /** @see IPhosphoNetXClientService#createAndLinkSamples(NewSample, List) */
+ public void createAndLinkSamples(NewSample newBiologicalSample,
+ List<Sample> msInjectionSamples, AsyncCallback<Void> callback);
+
/** @see IPhosphoNetXClientService#getTreatmentTypeVocabulary() */
public void getTreatmentTypeVocabulary(AsyncCallback<Vocabulary> callback);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java
index 9ebbb338054..3a88b2db57c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXModule.java
@@ -71,7 +71,7 @@ public class PhosphoNetXModule implements IModule
public DatabaseModificationAwareComponent createComponent(
IViewContext<IPhosphoNetXClientServiceAsync> context)
{
- return DatabaseModificationAwareComponent.wrapUnaware(new MsInjectionSampleAnnotationWizard(context));
+ return DatabaseModificationAwareComponent.create(new MsInjectionSampleAnnotationWizard(context));
}
public String tryGetLink()
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleChoosingPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
index 7f25c66295f..ccd692ba732 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
@@ -22,7 +22,6 @@ import com.extjs.gxt.ui.client.data.ModelData;
import com.extjs.gxt.ui.client.event.Listener;
import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.Label;
import com.extjs.gxt.ui.client.widget.layout.RowData;
@@ -49,9 +48,7 @@ public class BiologicalSampleChoosingPage extends WizardPage<MsInjectionSampleAn
{
super(viewContext, MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CHOOSING, model);
this.viewContext = viewContext;
- setLeftContentBy(new Html(
- "Annotating <tt>MS_INJECTION</tt> sample by choosing one biological sample means " +
- "that all properties of the biological sample is also for the <tt>MS_INJECTION</tt> to be annotated."));
+ setLeftContentByDictionary();
}
@Override
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleCreatingPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
index 6cf175b130e..c8b9dc2647b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
@@ -16,10 +16,33 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard;
-import com.extjs.gxt.ui.client.widget.Html;
+import java.util.Iterator;
+import java.util.List;
+import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
+import com.extjs.gxt.ui.client.event.SelectionChangedListener;
+import com.extjs.gxt.ui.client.util.Margins;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+import com.google.gwt.event.dom.client.ClickEvent;
+import com.google.gwt.event.dom.client.ClickHandler;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.SampleTypeDisplayID;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.SampleTypeModel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.SpaceSelectionWidget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CodeFieldWithGenerator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField.ExperimentChooserFieldAdaptor;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.sample.SampleTypeSelectionWidget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.ClickableFormPanel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.sample.AbstractGenericSampleRegisterEditForm;
+import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.sample.SamplePropertyEditor;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
/**
@@ -30,12 +53,113 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNet
public class BiologicalSampleCreatingPage extends WizardPage<MsInjectionSampleAnnotationModel>
{
+ private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+ private ClickableFormPanel formPanel;
+ private SampleTypeSelectionWidget sampleTypeSelectionWidget;
+ private SampleType sampleType;
+ private CodeFieldWithGenerator codeField;
+ private SpaceSelectionWidget spaceSelectionWidget;
+ private SamplePropertyEditor samplePropertyEditor;
+ private ExperimentChooserFieldAdaptor experimentField;
+
public BiologicalSampleCreatingPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
MsInjectionSampleAnnotationModel model)
{
super(viewContext, MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CREATING, model);
- setLeftContentBy(new Html(
- "Annotating <tt>MS_INJECTION</tt> sample by creating a new biological sample means ..."));
+ this.viewContext = viewContext;
+ setLeftContentByDictionary();
+ }
+
+ @Override
+ public void init()
+ {
+ formPanel = new ClickableFormPanel();
+ formPanel.setHeaderVisible(false);
+ sampleTypeSelectionWidget = new SampleTypeSelectionWidget(viewContext, "bio-samp", true,
+ SampleTypeDisplayID.SAMPLE_REGISTRATION, null)
+ {
+
+ @Override
+ protected void filterTypes(List<SampleType> types)
+ {
+ for (Iterator<SampleType> iterator = types.iterator(); iterator.hasNext();)
+ {
+ SampleType type = iterator.next();
+ if (type.getCode().startsWith("BIO") == false)
+ {
+ iterator.remove();
+ }
+ }
+ }
+ };
+ sampleTypeSelectionWidget.addSelectionChangedListener(new SelectionChangedListener<SampleTypeModel>()
+ {
+
+ @Override
+ public void selectionChanged(SelectionChangedEvent<SampleTypeModel> se)
+ {
+ SampleType sampleTypeOrNull = sampleTypeSelectionWidget.tryGetSelectedSampleType();
+ if (sampleTypeOrNull != null)
+ {
+ onSampleTypeChanged(sampleTypeOrNull);
+ }
+ }
+ });
+ formPanel.add(sampleTypeSelectionWidget);
+ addToRightContent(formPanel, new RowData(1, 500, new Margins(10)));
+ }
+
+ protected void onSampleTypeChanged(SampleType type)
+ {
+ this.sampleType = type;
+ formPanel.removeAll();
+ formPanel.add(sampleTypeSelectionWidget);
+ codeField =
+ new CodeFieldWithGenerator(viewContext, viewContext.getMessage(Dict.CODE),
+ type.getGeneratedCodePrefix(), type.isAutoGeneratedCode());
+ boolean codeReadonly = type.isAutoGeneratedCode();
+ codeField.setReadOnly(codeReadonly);
+ codeField.setHideTrigger(codeReadonly);
+ formPanel.add(codeField);
+ List<SampleTypePropertyType> types = type.getAssignedPropertyTypes();
+ spaceSelectionWidget =
+ new SpaceSelectionWidget(viewContext, getId(), true, false, viewContext.getModel()
+ .getSessionContext().getUser().getHomeGroupCode());
+ FieldUtil.markAsMandatory(spaceSelectionWidget);
+ formPanel.add(spaceSelectionWidget);
+ String label = viewContext.getMessage(Dict.EXPERIMENT);
+ experimentField = ExperimentChooserField.create(label, false, null,
+ viewContext.getCommonViewContext());
+ formPanel.add(experimentField.getChooserField());
+
+ samplePropertyEditor = new SamplePropertyEditor("bio-s", viewContext.getCommonViewContext());
+ samplePropertyEditor.initWithoutProperties(types);
+ samplePropertyEditor.addPropertyFieldsWithFieldsetToPanel(formPanel);
+ formPanel.layout();
+ formPanel.addClickListener(new ClickHandler()
+ {
+ public void onClick(ClickEvent event)
+ {
+ enableNextButton(formPanel.isValid());
+ }
+ });
+ }
+
+ @Override
+ public void deactivate()
+ {
+ String identifier =
+ AbstractGenericSampleRegisterEditForm.createSampleIdentifier(spaceSelectionWidget,
+ codeField);
+ String experimentIdentifierOrNull = experimentField.getChooserField().getValue();
+ List<IEntityProperty> properties = samplePropertyEditor.extractProperties();
+ model.defineBiologicalSample(sampleType, identifier, experimentIdentifierOrNull, properties);
+ }
+
+ @Override
+ public void destroy()
+ {
+ spaceSelectionWidget.dispose();
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
index b44484d5dcc..2905c16ba3a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
@@ -29,23 +29,29 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncC
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.IWizardDataModel;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.IWizardState;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardWorkflowModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class MsInjectionSampleAnnotationModel implements IWizardDataModel
{
private final IViewContext<IPhosphoNetXClientServiceAsync> context;
+
private final WizardWorkflowModel workflowModel;
+
private List<Sample> msInjectionSamples = new ArrayList<Sample>();
-
+
private boolean chooseBiologicalSampleFlag;
+
private Sample biologicalSample;
-
+
+ private NewSample newBiologicalSample;
+
public MsInjectionSampleAnnotationModel(IViewContext<IPhosphoNetXClientServiceAsync> context)
{
this.context = context;
@@ -54,7 +60,7 @@ public class MsInjectionSampleAnnotationModel implements IWizardDataModel
workflowModel.addTransition(CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CHOOSING);
workflowModel.addTransition(CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CREATING);
}
-
+
public WizardWorkflowModel getWorkflow()
{
return workflowModel;
@@ -64,17 +70,17 @@ public class MsInjectionSampleAnnotationModel implements IWizardDataModel
{
return chooseBiologicalSampleFlag ? BIOLOGICAL_SAMPLE_CHOOSING : BIOLOGICAL_SAMPLE_CREATING;
}
-
+
public void setSelectedMsInjectionSample(List<Sample> samples)
{
msInjectionSamples = samples;
}
-
+
public List<Sample> getMsInjectionSamples()
{
return msInjectionSamples;
}
-
+
public void setChooseBiologicalSampleFlag(boolean flag)
{
chooseBiologicalSampleFlag = flag;
@@ -85,10 +91,24 @@ public class MsInjectionSampleAnnotationModel implements IWizardDataModel
this.biologicalSample = biologicalSample;
}
+ public void defineBiologicalSample(SampleType sampleType, String identifier,
+ String experimentIdentifierOrNull, List<IEntityProperty> properties)
+ {
+ newBiologicalSample = NewSample.createWithParents(identifier, sampleType, null, null);
+ newBiologicalSample.setProperties(properties.toArray(IEntityProperty.EMPTY_ARRAY));
+ newBiologicalSample.setExperimentIdentifier(experimentIdentifierOrNull);
+ }
+
public String finish()
{
VoidAsyncCallback<Void> callback = new VoidAsyncCallback<Void>(context);
- context.getService().linkSamples(biologicalSample, msInjectionSamples, callback);
+ if (chooseBiologicalSampleFlag)
+ {
+ context.getService().linkSamples(biologicalSample, msInjectionSamples, callback);
+ } else
+ {
+ context.getService().createAndLinkSamples(newBiologicalSample, msInjectionSamples, callback);
+ }
return msInjectionSamples.size() + " MS_INJECTION samples have been annotated.";
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
index d4893777d37..83ecb08375a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
@@ -21,7 +21,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
/**
- *
+ * Wizard for annotation MS_INJECTION samples.
*
* @author Franz-Josef Elmer
*/
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
index 1e8d921fa4c..4dc424bf051 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
@@ -23,7 +23,6 @@ import com.extjs.gxt.ui.client.data.ModelData;
import com.extjs.gxt.ui.client.event.Listener;
import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Html;
import com.extjs.gxt.ui.client.widget.Label;
import com.extjs.gxt.ui.client.widget.layout.RowData;
@@ -50,16 +49,7 @@ public class MsInjectionSampleChoosingPage extends WizardPage<MsInjectionSampleA
{
super(viewContext, MsInjectionAnnotationWizardState.MS_INJECTION_SAMPLE_CHOOSING, model);
this.viewContext = viewContext;
- setLeftContentBy(new Html(
- "MS data are added to openBIS in an automated process. "
- + "The corresponding data sets are associated with samples of type <tt>MS_INJECTION</tt>."
- + "<p>Before MS data of such samples can be processed in a protein identification pipeline "
- + "they have to be <b>annotated</b>. In the terminology of openBIS this means: "
- + "An <tt>MS_INJECTION</tt> sample is linked to biological sample where "
- + "the biological sample is the parent and the <tt>MS_INJECTION</tt> sample is the child. "
- + "The biological sample has all annotations. "
- + "They define the scientific context of proteins found. "
- + "<p>This wizard helps you add these important annotations to openBIS."));
+ setLeftContentByDictionary();
}
@Override
@@ -80,7 +70,7 @@ public class MsInjectionSampleChoosingPage extends WizardPage<MsInjectionSampleA
}
});
- addToRightContent(sampleGrid, new RowData(1, 500, new Margins(20, 10, 10, 10)));
+ addToRightContent(sampleGrid, new RowData(1, 400, new Margins(20, 10, 10, 10)));
}
@Override
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/QuestionPage.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/QuestionPage.java
index 651f2a05755..d271778980e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/QuestionPage.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/QuestionPage.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard;
import com.extjs.gxt.ui.client.util.Margins;
-import com.extjs.gxt.ui.client.widget.Html;
+import com.extjs.gxt.ui.client.widget.Label;
import com.extjs.gxt.ui.client.widget.form.Radio;
import com.extjs.gxt.ui.client.widget.form.RadioGroup;
import com.extjs.gxt.ui.client.widget.layout.RowData;
@@ -41,10 +41,10 @@ public class QuestionPage extends WizardPage<MsInjectionSampleAnnotationModel>
MsInjectionSampleAnnotationModel model)
{
super(viewContext, MsInjectionAnnotationWizardState.CHOOSE_OR_CREATE_QUESTION, model);
- setLeftContentBy(new Html(
- "Annotating the <tt>MS_INJECTION</tt> samples you have chosen means to link them to a <b>biological sample</b>. "
- + "You can choose an existing biological sample or you can create a new one."));
- radioGroup = new RadioGroup("What do you want to annotate your samples?");
+ setLeftContentByDictionary();
+ addToRightContent(new Label("What do you want to annotate your samples?"), new RowData(1,
+ -1, new Margins(10)));
+ radioGroup = new RadioGroup();
radioGroup.setFieldLabel("choose");
chooseSampleRadioButton = new Radio();
chooseSampleRadioButton.setBoxLabel("I want to choose an existing biological sample.");
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 be7e8db6aa9..158ecaa7447 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
@@ -40,10 +40,26 @@ var phosphonetx = {
// MS_INJECTION annotation wizard
+ MS_INJECTION_SAMPLE_CHOOSING_left_content: "MS data are added to openBIS in an automated process. "
+ + "The corresponding data sets are associated with samples of type <tt>MS_INJECTION</tt>."
+ + "<p>Before MS data of such samples can be processed in a protein identification pipeline "
+ + "they have to be <b>annotated</b>. In the terminology of openBIS this means: "
+ + "An <tt>MS_INJECTION</tt> sample is linked to a biological sample where "
+ + "the biological sample is the parent and the <tt>MS_INJECTION</tt> sample is the child. "
+ + "The biological sample has all annotations (called properties in openBIS). "
+ + "They define the scientific context of proteins found. "
+ + "<p>This wizard helps you adding these important annotations to openBIS.",
openbis_parentless_ms_injection_sample_main_IDENTIFIER: "MS_INJECTION Sample",
openbis_parentless_ms_injection_sample_main_REGISTRATION_DATE: "Registration Date",
+ CHOOSE_OR_CREATE_QUESTION_left_content: "Annotating the <tt>MS_INJECTION</tt> samples you have chosen "
+ + "means to link them to a <b>biological sample</b>. "
+ + "You can choose an existing biological sample or you can create a new one.",
+ BIOLOGICAL_SAMPLE_CHOOSING_left_content: "Annotating <tt>MS_INJECTION</tt> sample by choosing one biological sample means "
+ + "that all properties of the biological sample is also for the <tt>MS_INJECTION</tt> to be annotated.",
openbis_biological_sample_main_IDENTIFIER: "Biological Sample",
openbis_biological_sample_main_REGISTRATION_DATE: "Registration Date",
+ BIOLOGICAL_SAMPLE_CREATING_left_content: "Annotating <tt>MS_INJECTION</tt> sample by creating a new biological sample means "
+ + "mainly specifying properties of a freshly created biological sample in openBIS.",
// RawDataSample Browser
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index 82ab5321db3..f569b8264b1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -52,6 +52,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
@@ -193,8 +194,22 @@ public class PhosphoNetXClientService extends AbstractClientService implements
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
String sessionToken = getSessionToken();
+ linkSamples(sessionToken, parentSample.getIdentifier(), childSamples);
+ }
+
+ public void createAndLinkSamples(NewSample newBiologicalSample, List<Sample> msInjectionSamples)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ String sessionToken = getSessionToken();
+ List<NewAttachment> noAttachments = Collections.<NewAttachment>emptyList();
+ genericServer.registerSample(sessionToken, newBiologicalSample, noAttachments);
+ linkSamples(sessionToken, newBiologicalSample.getIdentifier(), msInjectionSamples);
+ }
+
+ private void linkSamples(String sessionToken, String identifier, List<Sample> childSamples)
+ {
String[] parents = new String[]
- { parentSample.getIdentifier() };
+ { identifier };
for (Sample childSample : childSamples)
{
SampleIdentifier childSampleIdentifier =
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/BiologicalSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/BiologicalSampleProvider.java
index 25ceb8c7b81..9da3f00c18e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/BiologicalSampleProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/BiologicalSampleProvider.java
@@ -58,7 +58,7 @@ public class BiologicalSampleProvider extends AbstractCommonTableModelProvider<S
typeCriterion.setValue(CommonConstants.BIOLOGICAL_SAMPLE_PREFIX + "*");
DetailedSearchCriterion registratorCriterion = new DetailedSearchCriterion();
String userName = commonServer.tryGetSession(sessionToken).getUserName();
- registratorCriterion.setField(DetailedSearchField.createRegistratorField(""));
+ registratorCriterion.setField(DetailedSearchField.createRegistratorField());
registratorCriterion.setValue(userName);
criteria.setCriteria(Arrays.asList(typeCriterion, registratorCriterion));
List<Sample> samples = commonServer.searchForSamples(sessionToken, criteria);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
index f7983672404..dd56b8727d9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
@@ -61,8 +61,9 @@ public class ParentlessMsInjectionSampleProvider extends AbstractCommonTableMode
spaceCriterion.setValue(CommonConstants.MS_DATA_SPACE);
DetailedSearchCriterion registratorCriterion = new DetailedSearchCriterion();
String userName = commonServer.tryGetSession(sessionToken).getUserName();
- registratorCriterion.setField(DetailedSearchField.createRegistratorField(""));
+ registratorCriterion.setField(DetailedSearchField.createRegistratorField());
registratorCriterion.setValue(userName);
+ System.out.println("userName:"+userName);
criteria.setCriteria(Arrays.asList(typeCriterion, spaceCriterion, registratorCriterion));
List<Sample> samples = commonServer.searchForSamples(sessionToken, criteria);
TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
--
GitLab