From 719e185e1bb0e1a53200ead32640d47bc41dfcfd Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 10 Mar 2011 15:33:56 +0000
Subject: [PATCH] LMS-2103 Wizard framework and first useful version of an
annotation wizard
SVN: 20294
---
.../ui/grid/AbstractBrowserGrid.java | 21 +-
.../ui/grid/BrowserGridPagingToolBar.java | 11 ++
.../ui/wizard/IWizardDataModel.java | 40 ++++
.../application/ui/wizard/IWizardState.java | 27 +++
.../ui/wizard/IWizardStateChangeListener.java | 28 +++
.../client/application/ui/wizard/Wizard.java | 120 ++++++++++++
.../application/ui/wizard/WizardPage.java | 182 ++++++++++++++++++
.../ui/wizard/WizardWorkflowModel.java | 164 ++++++++++++++++
.../cisd/openbis/public/common-dictionary.js | 8 +
.../phosphonetx/AbundanceHandler.java | 3 +-
.../etlserver/phosphonetx/Constants.java | 2 -
.../DataSetInfoExtractorForMSInjection.java | 9 +-
.../web/client/IPhosphoNetXClientService.java | 11 ++
.../IPhosphoNetXClientServiceAsync.java | 14 ++
.../PhosphoNetXDisplayTypeIDGenerator.java | 4 +
.../client/application/PhosphoNetXModule.java | 46 ++++-
.../wizard/BiologicalSampleChoosingPage.java | 98 ++++++++++
.../wizard/BiologicalSampleCreatingPage.java | 41 ++++
.../wizard/BiologicalSampleGrid.java | 91 +++++++++
.../MsInjectionAnnotationWizardState.java | 29 +++
.../MsInjectionSampleAnnotationModel.java | 95 +++++++++
.../MsInjectionSampleAnnotationWizard.java | 41 ++++
.../wizard/MsInjectionSampleChoosingPage.java | 107 ++++++++++
.../ParentlessMsInjectionSampleGrid.java | 92 +++++++++
.../application/wizard/QuestionPage.java | 67 +++++++
.../dto/BiologicalSampleGridColumnIDs.java | 30 +++
...entlessMsInjectionSampleGridColumnIDs.java | 30 +++
.../web/public/phosphonetx-dictionary.js | 10 +
.../web/server/PhosphoNetXClientService.java | 56 +++++-
.../resultset/BiologicalSampleProvider.java | 78 ++++++++
.../ParentlessMsInjectionSampleProvider.java | 83 ++++++++
.../server/ProteomicsDataServiceInternal.java | 11 +-
.../phosphonetx/shared/CommonConstants.java | 31 +++
.../phosphonetx/AbundanceHandlerTest.java | 3 +-
...ataSetInfoExtractorForMSInjectionTest.java | 24 +--
.../ResultDataSetUploaderTest.java | 5 +-
.../ProteomicsDataServiceInternalTest.java | 8 +-
37 files changed, 1674 insertions(+), 46 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardDataModel.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardState.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardStateChangeListener.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/Wizard.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardPage.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardWorkflowModel.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleGrid.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/QuestionPage.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/BiologicalSampleGridColumnIDs.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/BiologicalSampleProvider.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/CommonConstants.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java
index 4ea4f5ce007..e398b4ec10d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/AbstractBrowserGrid.java
@@ -286,6 +286,16 @@ public abstract class AbstractBrowserGrid<T/* Entity */, M extends BaseEntityMod
});
}
+ public void removeConfigAndExportButtons()
+ {
+ pagingToolbar.removeConfigAndExportButtons();
+ }
+
+ public void removeFiltersButtons()
+ {
+ pagingToolbar.removeFiltersButtons();
+ }
+
private ICellListener<T> createShowEntityViewerLinkClickListener()
{
return new ICellListener<T>()
@@ -879,8 +889,7 @@ public abstract class AbstractBrowserGrid<T/* Entity */, M extends BaseEntityMod
if (show)
{
int logId = log("adding filters");
- bottomToolbars.insert(filterToolbar, 0);
- bottomToolbars.layout();
+ showFiltersBar();
viewContext.logStop(logId);
} else
{
@@ -893,6 +902,12 @@ public abstract class AbstractBrowserGrid<T/* Entity */, M extends BaseEntityMod
};
}
+ protected void showFiltersBar()
+ {
+ bottomToolbars.insert(filterToolbar, 0);
+ bottomToolbars.layout();
+ }
+
protected static interface ISelectedEntityInvoker<M>
{
void invoke(M selectedItem, boolean keyPressed);
@@ -1039,7 +1054,7 @@ public abstract class AbstractBrowserGrid<T/* Entity */, M extends BaseEntityMod
});
}
- private void addGridSelectionChangeListener(Listener<SelectionChangedEvent<ModelData>> listener)
+ public void addGridSelectionChangeListener(Listener<SelectionChangedEvent<ModelData>> listener)
{
grid.getSelectionModel().addListener(Events.SelectionChange, listener);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/BrowserGridPagingToolBar.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/BrowserGridPagingToolBar.java
index abe91f90d61..da645626fad 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/BrowserGridPagingToolBar.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/BrowserGridPagingToolBar.java
@@ -138,7 +138,18 @@ public final class BrowserGridPagingToolBar extends PagingToolBar
viewContext.logStop(logID);
setPagingComponentsHidden(true);
}
+
+ public void removeConfigAndExportButtons()
+ {
+ configButton.removeFromParent();
+ exportButton.removeFromParent();
+ }
+ public void removeFiltersButtons()
+ {
+ showFiltersButton.removeFromParent();
+ }
+
@Override
protected void onLoad(LoadEvent event)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardDataModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardDataModel.java
new file mode 100644
index 00000000000..c1221037723
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardDataModel.java
@@ -0,0 +1,40 @@
+/*
+ * 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.generic.client.web.client.application.ui.wizard;
+
+/**
+ * Basic interface to the data model behind a wizard.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IWizardDataModel
+{
+ /**
+ * Returns the workflow model.
+ */
+ public WizardWorkflowModel getWorkflow();
+
+ /**
+ * Determines at workflow branches the next state based on the specified current state.
+ */
+ public IWizardState determineNextState(IWizardState currentState);
+
+ /**
+ * Finishes the wizard, submit/commit data and return a success message for the user.
+ */
+ public String finish();
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardState.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardState.java
new file mode 100644
index 00000000000..c016e2f28a3
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardState.java
@@ -0,0 +1,27 @@
+/*
+ * 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.generic.client.web.client.application.ui.wizard;
+
+/**
+ * Marker interface for immutable value objects representing a state of a
+ * {@link WizardWorkflowModel}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IWizardState
+{
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardStateChangeListener.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardStateChangeListener.java
new file mode 100644
index 00000000000..289f1b96e6a
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/IWizardStateChangeListener.java
@@ -0,0 +1,28 @@
+/*
+ * 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.generic.client.web.client.application.ui.wizard;
+
+/**
+ * Interface to be implemented by classes interested in {@link IWizardState} changes in
+ * {@link WizardWorkflowModel}.
+ *
+ * @author Franz-Josef Elmer
+ */
+interface IWizardStateChangeListener
+{
+ void stateChanged(IWizardState previousStateOrNull, IWizardState currentStateOrNull);
+}
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
new file mode 100644
index 00000000000..b77b997516b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/Wizard.java
@@ -0,0 +1,120 @@
+/*
+ * 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.generic.client.web.client.application.ui.wizard;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+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;
+
+/**
+ * Container of {@link WizardPage} instance. Manages changing between pages.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Wizard<M extends IWizardDataModel> extends LayoutContainer
+{
+ private final CardLayout layout;
+
+ private final M model;
+
+ private final WizardWorkflowModel workflowModel;
+
+ private final Map<IWizardState, WizardPage<M>> pages =
+ new HashMap<IWizardState, WizardPage<M>>();
+
+ private final Set<WizardPage<M>> visitedPages = new HashSet<WizardPage<M>>();
+
+ /**
+ * Creates an instance for the specified wizard data model.
+ */
+ public Wizard(M model)
+ {
+ layout = new CardLayout();
+ setLayout(layout);
+ this.model = model;
+ workflowModel = model.getWorkflow();
+ workflowModel.addStateChangeListener(new IWizardStateChangeListener()
+ {
+ public void stateChanged(IWizardState previousStateOrNull,
+ IWizardState currentStateOrNull)
+ {
+ changePage(previousStateOrNull, currentStateOrNull);
+ }
+ });
+
+ }
+
+ public M getWizardDataModel()
+ {
+ return model;
+ }
+
+ /**
+ * Registers specified wizard page.
+ */
+ public void register(WizardPage<M> page)
+ {
+ pages.put(page.getWizardState(), page);
+ }
+
+ /**
+ * Starts this wizard.
+ */
+ public void start()
+ {
+ workflowModel.nextState();
+ }
+
+ private void changePage(IWizardState previousStateOrNull, IWizardState currentStateOrNull)
+ {
+ if (currentStateOrNull != null)
+ {
+ WizardPage<M> nextPage = pages.get(currentStateOrNull);
+ if (nextPage != null)
+ {
+ nextPage.activate();
+ if (visitedPages.contains(nextPage) == false)
+ {
+ nextPage.init();
+ visitedPages.add(nextPage);
+ add(nextPage);
+ }
+ layout.setActiveItem(nextPage);
+ }
+ } else if (workflowModel.hasNextState(currentStateOrNull) == false)
+ {
+ String message = model.finish();
+ MessageBox.info("Info", message, null);
+ for (WizardPage<M> page : visitedPages)
+ {
+ page.destroy();
+ }
+ Widget parent = getParent();
+ if (parent instanceof TabItem)
+ {
+ ((TabItem) parent).close();
+ }
+ }
+ }
+}
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
new file mode 100644
index 00000000000..07a175e3ecc
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardPage.java
@@ -0,0 +1,182 @@
+/*
+ * 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.generic.client.web.client.application.ui.wizard;
+
+import com.extjs.gxt.ui.client.Style.LayoutRegion;
+import com.extjs.gxt.ui.client.event.ButtonEvent;
+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.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
+import com.extjs.gxt.ui.client.widget.layout.BorderLayoutData;
+import com.extjs.gxt.ui.client.widget.layout.CenterLayout;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+import com.extjs.gxt.ui.client.widget.layout.RowLayout;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
+
+/**
+ * Base class of a page of a {@link Wizard}. Should be subclassed by overriding {@link #init()},
+ * {@link #deactivate()}, {@link #activate()}, {@link #destroy()} if needed.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class WizardPage<M extends IWizardDataModel> extends LayoutContainer
+{
+ 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";
+
+ protected final M model;
+ private final IWizardState state;
+ private final LayoutContainer leftContent;
+ private final LayoutContainer rightContent;
+ private Button previousButton;
+ private Button nextOrFinishButton;
+
+ /**
+ * Creates an instance for specified message provider, wizard state and wizard data model.
+ * Subclasses should create in the constructor only widget components which do not need
+ * sever calls. Components created/populated by server callbacks should be created in
+ * {@link #init()}.
+ */
+ public WizardPage(IMessageProvider messageProvider, IWizardState state, final M model)
+ {
+ super(new BorderLayout());
+ this.state = state;
+ this.model = model;
+ LayoutContainer leftCenterPanel = new LayoutContainer(new CenterLayout());
+ leftCenterPanel.setStyleAttribute("background-color", "white");
+ add(leftCenterPanel, new BorderLayoutData(LayoutRegion.WEST, 0.3f, 50, 200));
+ leftContent = new LayoutContainer(new RowLayout());
+ leftCenterPanel.add(leftContent);
+ ContentPanel rightPanel = new ContentPanel(new RowLayout());
+ rightPanel.setHeaderVisible(false);
+ add(rightPanel, new BorderLayoutData(LayoutRegion.CENTER));
+ LayoutContainer rightCenterPanel = new LayoutContainer(new RowLayout());
+ rightContent = new LayoutContainer(new RowLayout());
+ rightCenterPanel.add(rightContent, new RowData(1, 1, new Margins(10)));
+ rightPanel.add(rightCenterPanel);
+
+ final WizardWorkflowModel workflowModel = model.getWorkflow();
+ if (workflowModel.hasPreviousState(state))
+ {
+ previousButton = new Button(messageProvider.getMessage(PREVIOUS_BUTTON_LABEL_KEY));
+ previousButton.addSelectionListener(new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ workflowModel.previousState();
+ }
+ });
+ rightPanel.addButton(previousButton);
+ }
+ String key =
+ workflowModel.hasNextState(state) ? NEXT_BUTTON_LABEL_KEY : FINISH_BUTTON_LABEL_KEY;
+ nextOrFinishButton = new Button(messageProvider.getMessage(key));
+ nextOrFinishButton.setEnabled(false);
+ nextOrFinishButton.addSelectionListener(new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ deactivate();
+ workflowModel.nextState();
+ }
+ });
+ rightPanel.addButton(nextOrFinishButton);
+ }
+
+ IWizardState getWizardState()
+ {
+ return state;
+ }
+
+ /**
+ * Sets the content of the left hand part of this wizard page.
+ */
+ public void setLeftContentBy(Component component)
+ {
+ leftContent.removeAll();
+ leftContent.add(component, new RowData(1, 1, new Margins(10)));
+ }
+
+ /**
+ * Adds specified component to the right hand part of this wizard page. All components are
+ * layout by a vertical {@link RowLayout}.
+ */
+ public void addToRightContent(Component component, RowData layoutData)
+ {
+ rightContent.add(component, layoutData);
+ }
+
+ /**
+ * Enables/disables next/finish button.
+ */
+ public void enableNextButton(boolean enabled)
+ {
+ nextOrFinishButton.setEnabled(enabled);
+ }
+
+ /**
+ * Initializes this wizard page when it is shown the first time in the wizard.
+ * <p>
+ * This is a hook method which does nothing. It should be overridden if needed.
+ */
+ public void init()
+ {
+ }
+
+ /**
+ * Activates this page. This is called after {@link #deactivate()} has been invoked for the
+ * previous page (if any).
+ * <p>
+ * This is a hook method which does nothing. It should be overridden if needed.
+ */
+ public void activate()
+ {
+ }
+
+ /**
+ * Deactivates this page. This is called after the next/finish button has been pressed but
+ * before {@link #activate()} for the next page has been invoked. After invoking this method and
+ * before invocation of {@link #activate()} the method
+ * {@link IWizardDataModel#determineNextState(IWizardState)} will be invoked if more than one
+ * next states are possible.
+ * <p>
+ * This is a hook method which does nothing. It should be overridden if needed.
+ */
+ public void deactivate()
+ {
+ }
+
+ /**
+ * Destroys this page. It will be invoked when the wizard has successfully be finished. That is,
+ * after {@link IWizardDataModel#finish()} has been invoked. This method can be used to release
+ * resources.
+ * <p>
+ * This is a hook method which does nothing. It should be overridden if needed.
+ */
+ public void destroy()
+ {
+
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardWorkflowModel.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardWorkflowModel.java
new file mode 100644
index 00000000000..52d0b3e90fe
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/wizard/WizardWorkflowModel.java
@@ -0,0 +1,164 @@
+/*
+ * 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.generic.client.web.client.application.ui.wizard;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Stack;
+
+import com.google.gwt.core.client.JavaScriptException;
+
+/**
+ * Model of wizard workflow.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class WizardWorkflowModel
+{
+ private static final List<IWizardState> EMPTY_LIST = Arrays.<IWizardState>asList();
+
+ private final List<IWizardStateChangeListener> changeListeners =
+ new ArrayList<IWizardStateChangeListener>();
+
+ private final Map<IWizardState, List<IWizardState>> transitionsToNext =
+ new HashMap<IWizardState, List<IWizardState>>();
+
+ private final Map<IWizardState, List<IWizardState>> transitionsToPrevious =
+ new HashMap<IWizardState, List<IWizardState>>();
+
+ private final Stack<IWizardState> visitedStates = new Stack<IWizardState>();
+
+ private final IWizardDataModel dataModel;
+
+ private IWizardState initialState;
+
+ /**
+ * Creates an instance for the specified data model. The data model is needed to make
+ * decision at workflow branches.
+ */
+ public WizardWorkflowModel(IWizardDataModel dataModel)
+ {
+ this.dataModel = dataModel;
+ }
+
+ void addStateChangeListener(IWizardStateChangeListener stateChangeListener)
+ {
+ changeListeners.add(stateChangeListener);
+ }
+
+ /**
+ * Adds a transition from specified state to specified next state. For one state several
+ * transations can be added. In this branching case
+ * {@link IWizardDataModel#determineNextState(IWizardState)} will be invoked during execution
+ * of the workflow in order to determine which transition to follow.
+ */
+ public void addTransition(IWizardState state, IWizardState nextState)
+ {
+ List<IWizardState> nextStates = transitionsToNext.get(state);
+ if (nextStates == null)
+ {
+ nextStates = new ArrayList<IWizardState>();
+ transitionsToNext.put(state, nextStates);
+ }
+ nextStates.add(nextState);
+ List<IWizardState> previousStates = transitionsToPrevious.get(nextState);
+ if (previousStates == null)
+ {
+ previousStates = new ArrayList<IWizardState>();
+ transitionsToPrevious.put(nextState, previousStates);
+ }
+ previousStates.add(state);
+ if (initialState == null)
+ {
+ initialState = state;
+ }
+ }
+
+ void nextState()
+ {
+ List<IWizardState> nextStates = getNextStates();
+ if (nextStates.size() == 1)
+ {
+ setNextState(nextStates.get(0));
+ } else if (nextStates.size() > 1)
+ {
+ IWizardState nextState = dataModel.determineNextState(tryGetCurrentState());
+ if (nextStates.contains(nextState) == false)
+ {
+ throw new JavaScriptException("Error", "Next state " + nextState + " is not from "
+ + nextStates);
+ }
+ setNextState(nextState);
+ } else
+ {
+ fireStateChangeEvent(tryGetCurrentState(), null);
+ }
+ }
+
+ private void setNextState(IWizardState nextState)
+ {
+ IWizardState oldState = tryGetCurrentState();
+ visitedStates.push(nextState);
+ fireStateChangeEvent(oldState, nextState);
+ }
+
+ private void fireStateChangeEvent(IWizardState oldState, IWizardState nextState)
+ {
+ for (IWizardStateChangeListener listener : changeListeners)
+ {
+ listener.stateChanged(oldState, nextState);
+ }
+ }
+
+ boolean hasNextState(IWizardState state)
+ {
+ return transitionsToNext.get(state) != null;
+ }
+
+ private List<IWizardState> getNextStates()
+ {
+ IWizardState currentState = tryGetCurrentState();
+ if (currentState == null)
+ {
+ return initialState == null ? EMPTY_LIST : Arrays.asList(initialState);
+ }
+ List<IWizardState> nextStates = transitionsToNext.get(currentState);
+ return nextStates == null ? EMPTY_LIST : nextStates;
+ }
+
+ void previousState()
+ {
+ if (visitedStates.isEmpty() == false)
+ {
+ IWizardState oldState = visitedStates.pop();
+ fireStateChangeEvent(oldState, tryGetCurrentState());
+ }
+ }
+
+ boolean hasPreviousState(IWizardState state)
+ {
+ return transitionsToPrevious.get(state) != null;
+ }
+
+ IWizardState tryGetCurrentState()
+ {
+ return visitedStates.isEmpty() ? null : visitedStates.peek();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
index d27e0acc9c5..f2b9d96dec9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/common-dictionary.js
@@ -299,6 +299,14 @@ var common = {
default_update_value: "Update Value",
default_update_value_tooltip: "The value of the assigned property for all currently existing entities that didn't have any value for this property.",
+ //
+ // Wizard
+ //
+ wizard_page_previous_button_label: "< Previous",
+ wizard_page_next_button_label: "Next >",
+ wizard_page_finish_button_label: "Finish",
+
+
//
// Menu Titles
//
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
index 89e0906ad25..c296b81334b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
/**
* Handler of {@link Parameter} objects of type 'abundance'.
@@ -71,7 +72,7 @@ class AbundanceHandler extends AbstractHandler
this.experiment = experiment;
msData =
new SpaceIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
- Constants.MS_DATA_SPACE);
+ CommonConstants.MS_DATA_SPACE);
sampleType = new SampleType();
sampleType.setCode(Constants.SEARCH_SAMPLE_TYPE);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Constants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Constants.java
index 5f71ef1e0b3..23c6f7398e2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Constants.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Constants.java
@@ -25,7 +25,5 @@ public class Constants
{
public static final String NAMESPACE = "http://regis-web.systemsbiology.net/protXML";
- public static final String MS_DATA_SPACE = "MS_DATA";
-
public static final String SEARCH_SAMPLE_TYPE = "SEARCH";
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
index 93660860d5b..33497e439f5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
/**
* Data set info extractor for MS injection data sets. Information is extracted from a properties
@@ -77,8 +78,6 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
static final String EXPERIMENT_TYPE_CODE = "MS_INJECT";
- static final String SAMPLE_TYPE_CODE = "MS_INJECTION";
-
public DataSetInfoExtractorForMSInjection(Properties properties)
{
this(ServiceProvider.getOpenBISService());
@@ -96,7 +95,7 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
Properties sampleProperties =
Util.loadPropertiesFile(incomingDataSetPath, MS_INJECTION_PROPERTIES_FILE);
DataSetInformation info = new DataSetInformation();
- info.setSpaceCode(Constants.MS_DATA_SPACE);
+ info.setSpaceCode(CommonConstants.MS_DATA_SPACE);
info.setSampleCode(PropertyUtils.getMandatoryProperty(sampleProperties, SAMPLE_CODE_KEY));
SampleIdentifier sampleIdentifier = info.getSampleIdentifier();
ExperimentIdentifier experimentIdentifier = getExperimentIdentifier(sampleProperties);
@@ -140,7 +139,7 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
private long registerOrUpdateSample(SampleIdentifier sampleIdentifier,
ExperimentIdentifier experimentIdentifier, Properties properties)
{
- SampleType sampleType = service.getSampleType(SAMPLE_TYPE_CODE);
+ SampleType sampleType = service.getSampleType(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
Sample sample = service.tryGetSampleWithExperiment(sampleIdentifier);
String biologicalSampleIdentifier = properties.getProperty(BIOLOGICAL_SAMPLE_IDENTIFIER_KEY);
if (sample == null)
@@ -206,6 +205,6 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
PropertyUtils.getMandatoryProperty(msInjectionProperties, PROJECT_CODE_KEY);
String experimentCode =
PropertyUtils.getMandatoryProperty(msInjectionProperties, EXPERIMENT_CODE_KEY);
- return new ExperimentIdentifier(null, Constants.MS_DATA_SPACE, projectCode, experimentCode);
+ return new ExperimentIdentifier(null, CommonConstants.MS_DATA_SPACE, projectCode, experimentCode);
}
}
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 b00ad140cb5..2dbdbfe6c6f 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
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
@@ -53,6 +54,16 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPr
*/
public interface IPhosphoNetXClientService extends IClientService
{
+ public TypedTableResultSet<Sample> listParentlessMsInjectionSamples(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
+ throws UserFailureException;
+
+ public TypedTableResultSet<Sample> listBiologicalSamples(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
+ throws UserFailureException;
+
+ public void linkSamples(Sample parentSample, List<Sample> childSamples) 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 091d210db1f..baa9472aebc 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
@@ -21,6 +21,7 @@ import java.util.List;
import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
@@ -47,6 +48,19 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPr
*/
public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
{
+ /** @see IPhosphoNetXClientService#listParentlessMsInjectionSamples(DefaultResultSetConfig) */
+ public void listParentlessMsInjectionSamples(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria,
+ AsyncCallback<TypedTableResultSet<Sample>> callback);
+
+ /** @see IPhosphoNetXClientService#listBiologicalSamples(DefaultResultSetConfig) */
+ public void listBiologicalSamples(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria,
+ AsyncCallback<TypedTableResultSet<Sample>> callback);
+
+ /** @see IPhosphoNetXClientService#linkSamples(Sample, List) */
+ public void linkSamples(Sample parentSample, List<Sample> childSamples, 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/PhosphoNetXDisplayTypeIDGenerator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
index d39c574f91f..e4813ecb22d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
@@ -32,6 +32,10 @@ public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
DATA_SET_PROTEIN_BROWSER_GRID("data-set-protein-browser-grid"),
RAW_DATA_SAMPLE_BROWSER_GRID("raw-data-sample-browser-grid"),
+
+ PARENT_LESS_MS_INJECTION_SAMPLE_BROWSER_GRID("parent-less-ms-injection-sample-browser-grid"),
+
+ BIOLOGICAL_SAMPLE_BROWSER_GRID("biological-sample-browser-grid"),
;
private final String genericNameOrPrefix;
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 06a95db17c9..9ebbb338054 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
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
-import java.util.Collections;
import java.util.List;
import com.extjs.gxt.ui.client.widget.menu.MenuItem;
@@ -28,11 +28,15 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.Disposable
import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DatabaseModificationAwareComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ActionMenu;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.ITabActionMenuItemDefinition;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.menu.TabActionMenuItemFactory;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.plugin.IModule;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.MsInjectionSampleAnnotationWizard;
/**
* @author Franz-Josef Elmer
@@ -50,31 +54,59 @@ public class PhosphoNetXModule implements IModule
public List<? extends MenuItem> getMenuItems()
{
- return Collections.singletonList(TabActionMenuItemFactory.createActionMenu(viewContext, ID,
+ ActionMenu msInjectionSampleAnnotatingMenuItem = TabActionMenuItemFactory.createActionMenu(viewContext, ID,
new ITabActionMenuItemDefinition<IPhosphoNetXClientServiceAsync>()
{
public String getName()
{
- return "ALL_RAW_DATA_SAMPLES";
+ return "ANNOTATE_MS_INJECTION_SAMPLES";
}
public String getHelpPageTitle()
{
- return "MS INJECTION Data Overview";
+ return "Wizard for annotation MS INJECTION samples";
}
public DatabaseModificationAwareComponent createComponent(
IViewContext<IPhosphoNetXClientServiceAsync> context)
{
- return RawDataSampleGrid.create(context);
+ return DatabaseModificationAwareComponent.wrapUnaware(new MsInjectionSampleAnnotationWizard(context));
}
public String tryGetLink()
{
- return null;
+ URLMethodWithParameters url = new URLMethodWithParameters("");
+ url.addParameter(ViewLocator.ACTION_PARAMETER, getName());
+ return url.toString().substring(1);
}
- }));
+ });
+ ActionMenu msInjectionSampleBrowserMenuItem = TabActionMenuItemFactory.createActionMenu(viewContext, ID,
+ new ITabActionMenuItemDefinition<IPhosphoNetXClientServiceAsync>()
+ {
+
+ public String getName()
+ {
+ return "ALL_RAW_DATA_SAMPLES";
+ }
+
+ public String getHelpPageTitle()
+ {
+ return "MS INJECTION Data Overview";
+ }
+
+ public DatabaseModificationAwareComponent createComponent(
+ IViewContext<IPhosphoNetXClientServiceAsync> context)
+ {
+ return RawDataSampleGrid.create(context);
+ }
+
+ public String tryGetLink()
+ {
+ return null;
+ }
+ });
+ return Arrays.asList(msInjectionSampleAnnotatingMenuItem, msInjectionSampleBrowserMenuItem);
}
public String getName()
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
new file mode 100644
index 00000000000..7f25c66295f
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleChoosingPage.java
@@ -0,0 +1,98 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import java.util.List;
+
+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;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
+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.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ * Wizard for guiding the user to annotate an MS_INJECTION sample.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BiologicalSampleChoosingPage extends WizardPage<MsInjectionSampleAnnotationModel>
+{
+ private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+
+ private BiologicalSampleGrid sampleGrid;
+
+ public BiologicalSampleChoosingPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ MsInjectionSampleAnnotationModel model)
+ {
+ 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."));
+ }
+
+ @Override
+ public void init()
+ {
+ addToRightContent(
+ new Label(
+ "Please choose a biological sample as annotation of the MS_INJECTION samples selected previously:"),
+ new RowData(1, -1, new Margins(10)));
+
+ sampleGrid = new BiologicalSampleGrid(viewContext);
+ sampleGrid.addGridSelectionChangeListener(new Listener<SelectionChangedEvent<ModelData>>()
+ {
+ public void handleEvent(SelectionChangedEvent<ModelData> se)
+ {
+ List<ModelData> selection = se.getSelection();
+ boolean enabled = selection.size() == 1;
+ enableNextButton(enabled);
+ }
+
+ });
+ addToRightContent(sampleGrid, new RowData(1, 400, new Margins(20, 10, 10, 10)));
+ }
+
+ @Override
+ public void deactivate()
+ {
+ List<BaseEntityModel<TableModelRowWithObject<Sample>>> selectedItems =
+ sampleGrid.getSelectedItems();
+ if (selectedItems.isEmpty() == false)
+ {
+ model.setBiologicalSample(selectedItems.get(0).getBaseObject().getObjectOrNull());
+ }
+ }
+
+ @Override
+ public void destroy()
+ {
+ sampleGrid.dispose();
+ }
+
+
+
+}
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
new file mode 100644
index 00000000000..6cf175b130e
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleCreatingPage.java
@@ -0,0 +1,41 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import com.extjs.gxt.ui.client.widget.Html;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ * Wizard for guiding the user to annotate an MS_INJECTION sample.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BiologicalSampleCreatingPage extends WizardPage<MsInjectionSampleAnnotationModel>
+{
+
+ 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 ..."));
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleGrid.java
new file mode 100644
index 00000000000..05e13d3acab
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/BiologicalSampleGrid.java
@@ -0,0 +1,91 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import java.util.Arrays;
+import java.util.List;
+
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+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.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.PhosphoNetXDisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.BiologicalSampleGridColumnIDs;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BiologicalSampleGrid extends TypedTableGrid<Sample>
+{
+ private static final String PREFIX = GenericConstants.ID_PREFIX
+ + "biological_sample";
+
+ public static final String BROWSER_ID = PREFIX + "_main";
+
+ public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ public BiologicalSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID, true,
+ PhosphoNetXDisplayTypeIDGenerator.BIOLOGICAL_SAMPLE_BROWSER_GRID);
+ specificViewContext = viewContext;
+ removeConfigAndExportButtons();
+ removeFiltersButtons();
+ showFiltersBar();
+ setBorders(true);
+ }
+
+ @Override
+ protected void listTableRows(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> resultSetConfig,
+ AsyncCallback<TypedTableResultSet<Sample>> callback)
+ {
+ specificViewContext.getService().listBiologicalSamples(resultSetConfig, callback);
+ }
+
+ @Override
+ protected List<String> getColumnIdsOfFilters()
+ {
+ return Arrays.asList(BiologicalSampleGridColumnIDs.IDENTIFIER,
+ BiologicalSampleGridColumnIDs.REGISTRATION_DATE);
+ }
+
+ @Override
+ protected void prepareExportEntities(
+ TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ }
+
+ public void dispose()
+ {
+ asDisposableWithoutToolbar().dispose();
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java
new file mode 100644
index 00000000000..4afa1efd197
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionAnnotationWizardState.java
@@ -0,0 +1,29 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.IWizardState;
+
+/**
+ * States of wizard for annotating MS_INJECTION samples.
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum MsInjectionAnnotationWizardState implements IWizardState
+{
+ MS_INJECTION_SAMPLE_CHOOSING, CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CHOOSING, BIOLOGICAL_SAMPLE_CREATING;
+}
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
new file mode 100644
index 00000000000..b44484d5dcc
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationModel.java
@@ -0,0 +1,95 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CHOOSING;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.MsInjectionAnnotationWizardState.BIOLOGICAL_SAMPLE_CREATING;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.MsInjectionAnnotationWizardState.CHOOSE_OR_CREATE_QUESTION;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.MsInjectionAnnotationWizardState.MS_INJECTION_SAMPLE_CHOOSING;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.VoidAsyncCallback;
+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.Sample;
+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;
+
+ public MsInjectionSampleAnnotationModel(IViewContext<IPhosphoNetXClientServiceAsync> context)
+ {
+ this.context = context;
+ workflowModel = new WizardWorkflowModel(this);
+ workflowModel.addTransition(MS_INJECTION_SAMPLE_CHOOSING, CHOOSE_OR_CREATE_QUESTION);
+ workflowModel.addTransition(CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CHOOSING);
+ workflowModel.addTransition(CHOOSE_OR_CREATE_QUESTION, BIOLOGICAL_SAMPLE_CREATING);
+ }
+
+ public WizardWorkflowModel getWorkflow()
+ {
+ return workflowModel;
+ }
+
+ public IWizardState determineNextState(IWizardState currentState)
+ {
+ 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;
+ }
+
+ public void setBiologicalSample(Sample biologicalSample)
+ {
+ this.biologicalSample = biologicalSample;
+ }
+
+ public String finish()
+ {
+ VoidAsyncCallback<Void> callback = new VoidAsyncCallback<Void>(context);
+ context.getService().linkSamples(biologicalSample, 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
new file mode 100644
index 00000000000..d4893777d37
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleAnnotationWizard.java
@@ -0,0 +1,41 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.Wizard;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class MsInjectionSampleAnnotationWizard extends Wizard<MsInjectionSampleAnnotationModel>
+{
+ public MsInjectionSampleAnnotationWizard(IViewContext<IPhosphoNetXClientServiceAsync> context)
+ {
+ super(new MsInjectionSampleAnnotationModel(context));
+ MsInjectionSampleAnnotationModel wizardDataModel = getWizardDataModel();
+ register(new MsInjectionSampleChoosingPage(context, wizardDataModel));
+ register(new QuestionPage(context, wizardDataModel));
+ register(new BiologicalSampleChoosingPage(context, wizardDataModel));
+ register(new BiologicalSampleCreatingPage(context, wizardDataModel));
+ start();
+ }
+
+}
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
new file mode 100644
index 00000000000..1e8d921fa4c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/MsInjectionSampleChoosingPage.java
@@ -0,0 +1,107 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import java.util.ArrayList;
+import java.util.List;
+
+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;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.BaseEntityModel;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
+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.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ * Wizard for guiding the user to annotate an MS_INJECTION sample.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class MsInjectionSampleChoosingPage extends WizardPage<MsInjectionSampleAnnotationModel>
+{
+ private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
+
+ private ParentlessMsInjectionSampleGrid sampleGrid;
+
+ public MsInjectionSampleChoosingPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ MsInjectionSampleAnnotationModel model)
+ {
+ 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."));
+ }
+
+ @Override
+ public void init()
+ {
+ addToRightContent(new Label(
+ "Please choose one or more MS_INJECTION samples to be annotated:"), new RowData(1,
+ -1, new Margins(10)));
+
+ sampleGrid = new ParentlessMsInjectionSampleGrid(viewContext);
+ sampleGrid.addGridSelectionChangeListener(new Listener<SelectionChangedEvent<ModelData>>()
+ {
+ public void handleEvent(SelectionChangedEvent<ModelData> se)
+ {
+ List<ModelData> selection = se.getSelection();
+ boolean enabled = selection.size() > 0;
+ enableNextButton(enabled);
+ }
+
+ });
+ addToRightContent(sampleGrid, new RowData(1, 500, new Margins(20, 10, 10, 10)));
+ }
+
+ @Override
+ public void deactivate()
+ {
+ List<BaseEntityModel<TableModelRowWithObject<Sample>>> selectedItems =
+ sampleGrid.getSelectedItems();
+ ArrayList<Sample> samples = new ArrayList<Sample>();
+ for (BaseEntityModel<TableModelRowWithObject<Sample>> item : selectedItems)
+ {
+ samples.add(item.getBaseObject().getObjectOrNull());
+ }
+ model.setSelectedMsInjectionSample(samples);
+ }
+
+ @Override
+ public void destroy()
+ {
+ sampleGrid.dispose();
+ }
+
+
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java
new file mode 100644
index 00000000000..b66527acd85
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/ParentlessMsInjectionSampleGrid.java
@@ -0,0 +1,92 @@
+/*
+ * 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.phosphonetx.client.web.client.application.wizard;
+
+import java.util.Arrays;
+import java.util.List;
+
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.TypedTableGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+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.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.PhosphoNetXDisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ParentlessMsInjectionSampleGridColumnIDs;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ParentlessMsInjectionSampleGrid extends TypedTableGrid<Sample>
+{
+ private static final String PREFIX = GenericConstants.ID_PREFIX
+ + "parentless_ms_injection_sample";
+
+ public static final String BROWSER_ID = PREFIX + "_main";
+
+ public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ public ParentlessMsInjectionSampleGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID, true,
+ PhosphoNetXDisplayTypeIDGenerator.PARENT_LESS_MS_INJECTION_SAMPLE_BROWSER_GRID);
+ specificViewContext = viewContext;
+ removeConfigAndExportButtons();
+ removeFiltersButtons();
+ allowMultipleSelection();
+ showFiltersBar();
+ setBorders(true);
+ }
+
+ @Override
+ protected void listTableRows(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> resultSetConfig,
+ AsyncCallback<TypedTableResultSet<Sample>> callback)
+ {
+ specificViewContext.getService().listParentlessMsInjectionSamples(resultSetConfig, callback);
+ }
+
+ @Override
+ protected List<String> getColumnIdsOfFilters()
+ {
+ return Arrays.asList(ParentlessMsInjectionSampleGridColumnIDs.IDENTIFIER,
+ ParentlessMsInjectionSampleGridColumnIDs.REGISTRATION_DATE);
+ }
+
+ @Override
+ protected void prepareExportEntities(
+ TableExportCriteria<TableModelRowWithObject<Sample>> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ }
+
+ public void dispose()
+ {
+ asDisposableWithoutToolbar().dispose();
+ }
+
+}
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
new file mode 100644
index 00000000000..651f2a05755
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/wizard/QuestionPage.java
@@ -0,0 +1,67 @@
+/*
+ * 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.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.form.Radio;
+import com.extjs.gxt.ui.client.widget.form.RadioGroup;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.wizard.WizardPage;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class QuestionPage extends WizardPage<MsInjectionSampleAnnotationModel>
+{
+
+ private Radio chooseSampleRadioButton;
+ private RadioGroup radioGroup;
+
+ public QuestionPage(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ 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?");
+ radioGroup.setFieldLabel("choose");
+ chooseSampleRadioButton = new Radio();
+ chooseSampleRadioButton.setBoxLabel("I want to choose an existing biological sample.");
+ chooseSampleRadioButton.setValue(true);
+ radioGroup.add(chooseSampleRadioButton);
+ Radio createSampleRadioButton = new Radio();
+ createSampleRadioButton.setBoxLabel("I want to create a new biological sample.");
+ radioGroup.add(createSampleRadioButton);
+ addToRightContent(radioGroup, new RowData(1, -1, new Margins(10)));
+ enableNextButton(true);
+ }
+
+ @Override
+ public void deactivate()
+ {
+ model.setChooseBiologicalSampleFlag(radioGroup.getValue().equals(chooseSampleRadioButton));
+ }
+
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/BiologicalSampleGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/BiologicalSampleGridColumnIDs.java
new file mode 100644
index 00000000000..abe46fe8381
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/BiologicalSampleGridColumnIDs.java
@@ -0,0 +1,30 @@
+/*
+ * 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.phosphonetx.client.web.client.dto;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.ParentlessMsInjectionSampleGrid;
+
+/**
+ * IDs of columns of {@link ParentlessMsInjectionSampleGrid}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BiologicalSampleGridColumnIDs
+{
+ public static final String IDENTIFIER = "IDENTIFIER";
+ public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java
new file mode 100644
index 00000000000..5c4effab2f8
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ParentlessMsInjectionSampleGridColumnIDs.java
@@ -0,0 +1,30 @@
+/*
+ * 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.phosphonetx.client.web.client.dto;
+
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.wizard.ParentlessMsInjectionSampleGrid;
+
+/**
+ * IDs of columns of {@link ParentlessMsInjectionSampleGrid}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ParentlessMsInjectionSampleGridColumnIDs
+{
+ public static final String IDENTIFIER = "IDENTIFIER";
+ public static final String REGISTRATION_DATE = "REGISTRATION_DATE";
+}
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 b37959b0106..be7e8db6aa9 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
@@ -38,8 +38,18 @@ var phosphonetx = {
// SampleAbudndance Browser
abundance: "Abundance",
+ // MS_INJECTION annotation wizard
+
+ openbis_parentless_ms_injection_sample_main_IDENTIFIER: "MS_INJECTION Sample",
+ openbis_parentless_ms_injection_sample_main_REGISTRATION_DATE: "Registration Date",
+ openbis_biological_sample_main_IDENTIFIER: "Biological Sample",
+ openbis_biological_sample_main_REGISTRATION_DATE: "Registration Date",
+
+
// RawDataSample Browser
+ ANNOTATE_MS_INJECTION_SAMPLES_menu_item: "Annotate MS INJECTION Samples",
+ ANNOTATE_MS_INJECTION_SAMPLES_tab_label: "MS INJECTION Samples Annotation Wizard",
ALL_RAW_DATA_SAMPLES_menu_item: "All MS INJECTION Samples",
ALL_RAW_DATA_SAMPLES_tab_label: "MS INJECTION Samples and Related Biological Samples",
openbis_raw_data_sample_browser_CODE: "MS INJECTION Sample",
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 516ebbf6b0f..82ab5321db3 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
@@ -20,6 +20,7 @@ import static ch.systemsx.cisd.common.utilities.SystemTimeProvider.SYSTEM_TIME_P
import java.io.Serializable;
import java.lang.reflect.Method;
+import java.util.Collections;
import java.util.List;
import javax.annotation.Resource;
@@ -38,6 +39,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.IFreeSpaceProvider;
import ch.systemsx.cisd.common.filesystem.SimpleFreeSpaceProvider;
import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
@@ -45,15 +47,23 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSe
import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.DataProviderAdapter;
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.UserFailureExceptionTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
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.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.WebClientConfiguration;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.util.CacheManager;
import ch.systemsx.cisd.openbis.generic.shared.util.ICacheManager;
import ch.systemsx.cisd.openbis.generic.shared.util.Key;
+import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.BuildAndEnvironmentInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.Constants;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
@@ -62,7 +72,9 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListPro
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.resultset.BiologicalSampleProvider;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.resultset.DataSetProteinProvider;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.resultset.ParentlessMsInjectionSampleProvider;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.resultset.ProteinSequenceProvider;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.resultset.ProteinSummaryProvider;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CacheData;
@@ -85,7 +97,13 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPr
public class PhosphoNetXClientService extends AbstractClientService implements
IPhosphoNetXClientService, InitializingBean
{
- private static final String CACHE_VERSION = "1"; // Sprint S97
+ private static final String CACHE_VERSION = Integer.toString(ServiceVersionHolder.VERSION);
+
+ @Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
+ private ICommonServer commonServer;
+
+ @Resource(name = ch.systemsx.cisd.openbis.plugin.generic.shared.ResourceNames.GENERIC_PLUGIN_SERVER)
+ private IGenericServer genericServer;
@Resource(name = ResourceNames.PHOSPHONETX_PLUGIN_SERVER)
@Private
@@ -154,6 +172,42 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return BuildAndEnvironmentInfo.INSTANCE.getFullVersion();
}
+ public TypedTableResultSet<Sample> listParentlessMsInjectionSamples(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ String sessionToken = getSessionToken();
+ return listEntities(new ParentlessMsInjectionSampleProvider(commonServer, sessionToken),
+ criteria);
+ }
+
+ public TypedTableResultSet<Sample> listBiologicalSamples(
+ DefaultResultSetConfig<String, TableModelRowWithObject<Sample>> criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ String sessionToken = getSessionToken();
+ return listEntities(new BiologicalSampleProvider(commonServer, sessionToken), criteria);
+ }
+
+ public void linkSamples(Sample parentSample, List<Sample> childSamples)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ String sessionToken = getSessionToken();
+ String[] parents = new String[]
+ { parentSample.getIdentifier() };
+ for (Sample childSample : childSamples)
+ {
+ SampleIdentifier childSampleIdentifier =
+ SampleIdentifierFactory.parse(childSample.getIdentifier());
+ genericServer.updateSample(
+ sessionToken,
+ new SampleUpdatesDTO(new TechId(childSample), Collections
+ .<IEntityProperty> emptyList(), null, Collections
+ .<NewAttachment> emptyList(), childSample.getModificationDate(),
+ childSampleIdentifier, null, parents));
+ }
+ }
+
public Vocabulary getTreatmentTypeVocabulary()
{
final String sessionToken = getSessionToken();
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
new file mode 100644
index 00000000000..25ceb8c7b81
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/BiologicalSampleProvider.java
@@ -0,0 +1,78 @@
+/*
+ * 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.phosphonetx.client.web.server.resultset;
+
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.BiologicalSampleGridColumnIDs.IDENTIFIER;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.BiologicalSampleGridColumnIDs.REGISTRATION_DATE;
+
+import java.util.Arrays;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractCommonTableModelProvider;
+import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriterion;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchField;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleAttributeSearchFieldKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
+import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
+
+/**
+ * Provider of biological samples registered by the user. A biological sample is a sample with
+ * sample type code starting with BIO.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BiologicalSampleProvider extends AbstractCommonTableModelProvider<Sample>
+{
+ public BiologicalSampleProvider(ICommonServer commonServer, String sessionToken)
+ {
+ super(commonServer, sessionToken);
+ }
+
+ @Override
+ protected TypedTableModel<Sample> createTableModel(int maxSize)
+ {
+ DetailedSearchCriteria criteria = new DetailedSearchCriteria();
+ criteria.setConnection(SearchCriteriaConnection.MATCH_ALL);
+ DetailedSearchCriterion typeCriterion = new DetailedSearchCriterion();
+ typeCriterion.setField(DetailedSearchField
+ .createAttributeField(SampleAttributeSearchFieldKind.SAMPLE_TYPE));
+ typeCriterion.setValue(CommonConstants.BIOLOGICAL_SAMPLE_PREFIX + "*");
+ DetailedSearchCriterion registratorCriterion = new DetailedSearchCriterion();
+ String userName = commonServer.tryGetSession(sessionToken).getUserName();
+ registratorCriterion.setField(DetailedSearchField.createRegistratorField(""));
+ registratorCriterion.setValue(userName);
+ criteria.setCriteria(Arrays.asList(typeCriterion, registratorCriterion));
+ List<Sample> samples = commonServer.searchForSamples(sessionToken, criteria);
+ TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
+ builder.addColumn(IDENTIFIER);
+ builder.addColumn(REGISTRATION_DATE);
+ for (Sample sample : samples)
+ {
+ builder.addRow(sample);
+ builder.column(IDENTIFIER).addString(sample.getIdentifier());
+ builder.column(REGISTRATION_DATE).addDate(sample.getRegistrationDate());
+ builder.columnGroup("PROPERTY").addProperties(sample.getProperties());
+ }
+ return builder.getModel();
+ }
+
+}
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
new file mode 100644
index 00000000000..f7983672404
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ParentlessMsInjectionSampleProvider.java
@@ -0,0 +1,83 @@
+/*
+ * 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.phosphonetx.client.web.server.resultset;
+
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ParentlessMsInjectionSampleGridColumnIDs.IDENTIFIER;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ParentlessMsInjectionSampleGridColumnIDs.REGISTRATION_DATE;
+
+import java.util.Arrays;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractCommonTableModelProvider;
+import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriterion;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchField;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleAttributeSearchFieldKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SearchCriteriaConnection;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
+import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
+
+/**
+ * Provider of MS_INJECTION samples registered for the user.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ParentlessMsInjectionSampleProvider extends AbstractCommonTableModelProvider<Sample>
+{
+ public ParentlessMsInjectionSampleProvider(ICommonServer commonServer, String sessionToken)
+ {
+ super(commonServer, sessionToken);
+ }
+
+ @Override
+ protected TypedTableModel<Sample> createTableModel(int maxSize)
+ {
+ DetailedSearchCriteria criteria = new DetailedSearchCriteria();
+ criteria.setConnection(SearchCriteriaConnection.MATCH_ALL);
+ DetailedSearchCriterion typeCriterion = new DetailedSearchCriterion();
+ typeCriterion.setField(DetailedSearchField
+ .createAttributeField(SampleAttributeSearchFieldKind.SAMPLE_TYPE));
+ typeCriterion.setValue(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
+ DetailedSearchCriterion spaceCriterion = new DetailedSearchCriterion();
+ spaceCriterion.setField(DetailedSearchField
+ .createAttributeField(SampleAttributeSearchFieldKind.GROUP));
+ spaceCriterion.setValue(CommonConstants.MS_DATA_SPACE);
+ DetailedSearchCriterion registratorCriterion = new DetailedSearchCriterion();
+ String userName = commonServer.tryGetSession(sessionToken).getUserName();
+ registratorCriterion.setField(DetailedSearchField.createRegistratorField(""));
+ registratorCriterion.setValue(userName);
+ criteria.setCriteria(Arrays.asList(typeCriterion, spaceCriterion, registratorCriterion));
+ List<Sample> samples = commonServer.searchForSamples(sessionToken, criteria);
+ TypedTableModelBuilder<Sample> builder = new TypedTableModelBuilder<Sample>();
+ builder.addColumn(IDENTIFIER).withDefaultWidth(300);
+ builder.addColumn(REGISTRATION_DATE).withDefaultWidth(300);
+ for (Sample sample : samples)
+ {
+ if (sample.getGeneratedFrom() == null)
+ {
+ builder.addRow(sample);
+ builder.column(IDENTIFIER).addString(sample.getIdentifier());
+ builder.column(REGISTRATION_DATE).addDate(sample.getRegistrationDate());
+ }
+ }
+ return builder.getModel();
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
index 8ff7a36249b..dcb2734b5c9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
@@ -24,7 +24,6 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
-import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -56,6 +55,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ExperimentLoader;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleLoader;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.ParentSampleValidator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
@@ -67,12 +67,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDataServiceInternal> implements
IProteomicsDataServiceInternal
{
- @Private
- static final String SPACE_CODE = "MS_DATA";
-
- @Private
- static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
-
private static final IValidator<Sample> PARENT_SAMPLE_VALIDATOR = new ParentSampleValidator();
private static final IValidator<MsInjectionSample> RAW_DATA_SAMPLE_VALIDATOR =
@@ -230,7 +224,8 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
{
ISampleLoader sampleLoader = boFactory.createSampleLoader(session);
List<Sample> samples =
- sampleLoader.listSamplesWithParentsByTypeAndSpace(RAW_DATA_SAMPLE_TYPE, SPACE_CODE);
+ sampleLoader.listSamplesWithParentsByTypeAndSpace(
+ CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE, CommonConstants.MS_DATA_SPACE);
PersonPE person = session.tryGetPerson();
List<Sample> validSamples = new ArrayList<Sample>();
for (Sample sample : samples)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/CommonConstants.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/CommonConstants.java
new file mode 100644
index 00000000000..4d73efc2cd8
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/CommonConstants.java
@@ -0,0 +1,31 @@
+/*
+ * 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.phosphonetx.shared;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class CommonConstants
+{
+
+ public static final String MS_INJECTION_SAMPLE_TYPE_CODE = "MS_INJECTION";
+ public static final String BIOLOGICAL_SAMPLE_PREFIX = "BIO";
+ public static final String MS_DATA_SPACE = "MS_DATA";
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
index fb0d3744543..c79d75532b5 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
/**
* @author Franz-Josef Elmer
@@ -55,7 +56,7 @@ public class AbundanceHandlerTest extends AssertJUnit
private static final String EXPERIMENT_CODE = "E1";
private static final GroupIdentifier GROUP_IDENTIFIER = new GroupIdentifier((String) null,
- Constants.MS_DATA_SPACE);
+ CommonConstants.MS_DATA_SPACE);
private static final String PARAMETER_VALUE = "1234.5";
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
index 7aed4b784d2..65e69085298 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjectionTest.java
@@ -25,7 +25,6 @@ import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtracto
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.PARENT_TYPE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.PROJECT_CODE_KEY;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.SAMPLE_CODE_KEY;
-import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE;
import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForMSInjection.USER_KEY;
import java.io.File;
@@ -73,6 +72,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
/**
* @author Franz-Josef Elmer
@@ -86,11 +86,11 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
private static final String SAMPLE_CODE = "U09-1242";
private static final String SAMPLE_IDENTIFIER =
- DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + Constants.MS_DATA_SPACE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + CommonConstants.MS_DATA_SPACE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + SAMPLE_CODE;
private static final String EXPERIMENT_IDENTIFIER =
- DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + Constants.MS_DATA_SPACE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + CommonConstants.MS_DATA_SPACE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + PROJECT_CODE
+ DatabaseInstanceIdentifier.Constants.IDENTIFIER_SEPARATOR + EXPERIMENT_CODE;
@@ -297,7 +297,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
- assertEquals(Constants.MS_DATA_SPACE, info.getSpaceCode());
+ assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
assertEquals(SAMPLE_CODE, info.getSampleCode());
assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
List<NewProperty> dProps = info.getDataSetProperties();
@@ -332,7 +332,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
- assertEquals(Constants.MS_DATA_SPACE, info.getSpaceCode());
+ assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
assertEquals(SAMPLE_CODE, info.getSampleCode());
assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
List<NewProperty> dProps = info.getDataSetProperties();
@@ -364,7 +364,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
- assertEquals(Constants.MS_DATA_SPACE, info.getSpaceCode());
+ assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
assertEquals(SAMPLE_CODE, info.getSampleCode());
assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
List<NewProperty> dProps = info.getDataSetProperties();
@@ -397,7 +397,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
- assertEquals(Constants.MS_DATA_SPACE, info.getSpaceCode());
+ assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
assertEquals(SAMPLE_CODE, info.getSampleCode());
assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
List<NewProperty> dProps = info.getDataSetProperties();
@@ -436,7 +436,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
DataSetInformation info = extractor.getDataSetInformation(dataSet, service);
- assertEquals(Constants.MS_DATA_SPACE, info.getSpaceCode());
+ assertEquals(CommonConstants.MS_DATA_SPACE, info.getSpaceCode());
assertEquals(null, info.getSampleCode());
assertEquals(null, info.getSampleIdentifier());
assertEquals(EXPERIMENT_IDENTIFIER, info.getExperimentIdentifier().toString());
@@ -489,7 +489,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
{
{
ExperimentIdentifier identifier =
- new ExperimentIdentifier(null, Constants.MS_DATA_SPACE, PROJECT_CODE,
+ new ExperimentIdentifier(null, CommonConstants.MS_DATA_SPACE, PROJECT_CODE,
EXPERIMENT_CODE);
one(service).tryToGetExperiment(identifier);
Experiment experiment = new Experiment();
@@ -511,9 +511,9 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
context.checking(new Expectations()
{
{
- one(service).getSampleType(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
+ one(service).getSampleType(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
SampleType sampleType = new SampleType();
- sampleType.setCode(DataSetInfoExtractorForMSInjection.SAMPLE_TYPE_CODE);
+ sampleType.setCode(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE);
sampleType.setSampleTypePropertyTypes(Arrays.asList(sampleTypePropertyTypes));
will(returnValue(sampleType));
}
@@ -552,7 +552,7 @@ public class DataSetInfoExtractorForMSInjectionTest extends AbstractFileSystemTe
if (item instanceof NewSample)
{
NewSample sample = (NewSample) item;
- assertEquals(SAMPLE_TYPE_CODE, sample.getSampleType().getCode());
+ assertEquals(CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE, sample.getSampleType().getCode());
assertEquals(SAMPLE_IDENTIFIER, sample.getIdentifier());
assertEquals(EXPERIMENT_IDENTIFIER, sample
.getExperimentIdentifier());
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
index 71165afb4fc..d31c22ab65d 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
@@ -64,6 +64,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
/**
* @author Franz-Josef Elmer
@@ -242,7 +243,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
{
one(service).tryGetSampleWithExperiment(
new SampleIdentifier(new SpaceIdentifier(DB_INSTANCE,
- Constants.MS_DATA_SPACE), CELL_LYSATE1));
+ CommonConstants.MS_DATA_SPACE), CELL_LYSATE1));
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
sample.setPermId(CELL_LYSATE_PERM_ID1);
@@ -293,7 +294,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
p1.setName(PROTEIN_NAME1);
p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
p1.getParameters().add(new Parameter());
- final GroupIdentifier groupIdentifier = new GroupIdentifier(DB_INSTANCE, Constants.MS_DATA_SPACE);
+ final GroupIdentifier groupIdentifier = new GroupIdentifier(DB_INSTANCE, CommonConstants.MS_DATA_SPACE);
final SampleIdentifier sampleIdentifier =
new SampleIdentifier(groupIdentifier, CELL_LYSATE1);
final ListSamplesByPropertyCriteria criteria =
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
index b8f168f569e..fe247046c59 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
@@ -18,8 +18,6 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.PROCESSING;
import static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind.QUERIES;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.RAW_DATA_SAMPLE_TYPE;
-import static ch.systemsx.cisd.openbis.plugin.phosphonetx.server.ProteomicsDataServiceInternal.SPACE_CODE;
import java.util.ArrayList;
import java.util.Arrays;
@@ -55,14 +53,15 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleLoader;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.CommonConstants;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -348,7 +347,8 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
one(boFactory).createSampleLoader(SESSION);
will(returnValue(sampleLoader));
- one(sampleLoader).listSamplesWithParentsByTypeAndSpace(RAW_DATA_SAMPLE_TYPE, SPACE_CODE);
+ one(sampleLoader).listSamplesWithParentsByTypeAndSpace(
+ CommonConstants.MS_INJECTION_SAMPLE_TYPE_CODE, CommonConstants.MS_DATA_SPACE);
will(returnValue(samples));
one(experimentDAO).listExperimentsWithProperties(experimentIds);
--
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