Author: kono
Date: 2011-01-19 17:13:00 -0800 (Wed, 19 Jan 2011)
New Revision: 23523
Added:
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenu.java
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
Removed:
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/WebServiceClientManagerImpl.java
Modified:
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Major update version of web service API. Biomart client still needs some
refactoring to use this new API.
Deleted:
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/WebServiceClientManagerImpl.java
===================================================================
---
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/WebServiceClientManagerImpl.java
2011-01-20 01:12:41 UTC (rev 23522)
+++
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/WebServiceClientManagerImpl.java
2011-01-20 01:13:00 UTC (rev 23523)
@@ -1,116 +0,0 @@
-/*
- Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-package org.cytoscape.webservice.internal;
-
-import java.net.URI;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.cytoscape.io.webservice.WebServiceClient;
-import org.cytoscape.io.webservice.WebServiceClientManager;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-
-/**
- * Web Service Client Manager manages available web service
- * clients in Cytoscape. All clients will be loaded & registered through
- * Plugin Manager architecture.
- *
- *
- */
-public class WebServiceClientManagerImpl implements WebServiceClientManager {
-
- private static final Logger logger =
LoggerFactory.getLogger(WebServiceClientManagerImpl.class);
-
- // Clients available in Cytoscape.
- private final Map<URI, WebServiceClient<?>> clients;
-
-
- public WebServiceClientManagerImpl() {
- clients = new HashMap<URI, WebServiceClient<?>>();
- }
-
-
- /**
- * Register client to this manager.
- *
- * This will be used by Spring DM.
- *
- * @param client
- * @param props metadata from
- */
- public void registerClient(final WebServiceClient<?> client, Map props)
{
- if (client == null) {
- logger.warn("Could not register client: Web Service
Client is null.");
- return;
- }
-
- clients.put(client.getServiceLocation(), client);
- }
-
- /**
- * Unregister client from this manager.
- *
- * This will be called by Spring DM.
- *
- * @param client Client to be removed.
- * @param props Metadata for this client.
- */
- public void removeClient(WebServiceClient<?> client, Map props) {
- if (client == null) {
- logger.warn("No such client.");
- return;
- }
-
- clients.remove(client.getServiceLocation());
- client = null;
- }
-
-
- @Override public Set<WebServiceClient<?>> getAllClients() {
- return new HashSet<WebServiceClient<?>>(clients.values());
- }
-
-
- @Override public WebServiceClient<?> getClient(final URI serviceURI) {
- return clients.get(serviceURI);
- }
-
-
-
-}
Added:
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
===================================================================
---
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
(rev 0)
+++
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/UnifiedNetworkImportDialog.java
2011-01-20 01:13:00 UTC (rev 23523)
@@ -0,0 +1,761 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.webservice.internal.ui;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.BoxLayout;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.border.EmptyBorder;
+
+import org.cytoscape.io.webservice.NetworkImportWebServiceClient;
+import org.cytoscape.io.webservice.WebServiceClient;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+
+import com.sun.java.swing.plaf.gtk.GTKConstants.IconSize;
+
+/**
+ * Default GUI component for network import web service clients.
+ *
+ * @author kono
+ */
+public class UnifiedNetworkImportDialog extends JDialog {
+
+ private static final long serialVersionUID = 3333726113970459078L;
+
+// // This is a singleton.
+// private static final UnifiedNetworkImportDialog dialog;
+//
+// // Selected web service client ID
+// private String selectedClientID = null;
+//
+// // Task to run in the separate thread.
+// private WSNetworkImportTask task;
+//
+// // Key is display name, value is actual service name.
+// private Map<String, String> clientNames;
+//
+// // Client-Dependent GUI panels
+// private Map<String, Container> serviceUIPanels = new HashMap<String,
Container>();
+//
+// // Default icon for about dialog
+// private static final Icon DEF_ICON = new javax.swing.ImageIcon(
+//
Cytoscape.class.getResource("images/ximian/stock_internet-32.png"));
+//
+// private static CyLogger logger = CyLogger
+// .getLogger(UnifiedNetworkImportDialog.class);
+//
+// private int numDataSources = 0;
+// private int numClients = 0;
+//
+// private boolean cancelFlag = false;
+//
+// static {
+// dialog = new UnifiedNetworkImportDialog(Cytoscape.getDesktop(),
false);
+// }
+//
+// /**
+// * Display this standard GUI.
+// */
+// public static void showDialog() {
+// dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+// dialog.setVisible(true);
+// }
+//
+// /**
+// * Creates new form NetworkImportDialog
+// */
+// public UnifiedNetworkImportDialog(Frame parent, boolean modal) {
+// super(parent, modal);
+//
+// // Register as listener.
+//
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+//
+// initGUI();
+// }
+//
+// /**
+// * Resets the GUI w/ all new info.
+// */
+// public void resetGUI() {
+// this.getContentPane().removeAll();
+// initGUI();
+// }
+//
+// private void initGUI() {
+// clientNames = new HashMap<String, String>();
+//
+// List<WebServiceClient<?>> clients = WebServiceClientManager
+// .getAllClients();
+// for (WebServiceClient<?> client : clients) {
+// if (client instanceof NetworkImportWebServiceClient) {
+// numClients++;
+// }
+// }
+//
+// initComponents();
+// setDatasource();
+//
+// // If we have no data sources, show the install panel
+// getContentPane().setLayout(new BorderLayout());
+// if (numClients <= 1) {
+// this.getContentPane().add(installPanel,
BorderLayout.SOUTH);
+// }
+// if (numClients > 0) {
+// this.getContentPane().add(queryPanel,
BorderLayout.CENTER);
+// }
+//
+// this.pack();
+//
setProperty(clientNames.get(datasourceComboBox.getSelectedItem()));
+// selectedClientID = clientNames
+// .get(datasourceComboBox.getSelectedItem());
+//
+// // Initialize GUI panel.
+// datasourceComboBoxActionPerformed(null);
+// }
+//
+// /**
+// * This method is called from within the constructor to initialize the
form.
+// * WARNING: Do NOT modify this code. The content of this method is
always
+// * regenerated by the Form Editor.
+// */
+// private void initComponents() {
+// mainTabbedPane = new javax.swing.JTabbedPane();
+// searchTermScrollPane = new javax.swing.JScrollPane();
+// queryTextPane = new javax.swing.JTextPane();
+// propertyPanel = new javax.swing.JPanel();
+//
+// queryTextPane.setFont(new java.awt.Font("SansSerif", 0, 12));
+// queryTextPane.setText("Please enter search terms...");
+// searchTermScrollPane.setViewportView(queryTextPane);
+//
+// mainTabbedPane.addTab("Query", searchTermScrollPane);
+//
+// org.jdesktop.layout.GroupLayout propertyPanelLayout = new
org.jdesktop.layout.GroupLayout(
+// propertyPanel);
+// propertyPanel.setLayout(propertyPanelLayout);
+// propertyPanelLayout.setHorizontalGroup(propertyPanelLayout
+//
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+// .add(0, 408, Short.MAX_VALUE));
+// propertyPanelLayout.setVerticalGroup(propertyPanelLayout
+//
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+// .add(0, 303, Short.MAX_VALUE));
+//
+// propertyScrollPane = new JScrollPane();
+// propertyScrollPane.setViewportView(propertyPanel);
+// mainTabbedPane.addTab("Search Property", propertyScrollPane);
+//
+// titlePanel = new javax.swing.JPanel();
+// titleIconLabel = new javax.swing.JLabel();
+// datasourcePanel = new javax.swing.JPanel();
+// datasourceLabel = new javax.swing.JLabel();
+// datasourceComboBox = new javax.swing.JComboBox();
+// aboutButton = new javax.swing.JButton();
+// buttonPanel = new javax.swing.JPanel();
+// searchButton = new javax.swing.JButton();
+// cancelButton = new javax.swing.JButton();
+// clearButton = new javax.swing.JButton();
+// dataQueryPanel = new javax.swing.JPanel();
+//
+// setTitle("Import Network from Database");
+//
+//
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+//
+// titlePanel.setBackground(new java.awt.Color(0, 0, 0));
+//
+// titleIconLabel.setIcon(new javax.swing.ImageIcon(Cytoscape.class
+// .getResource("images/networkImportIcon.png")));
// NOI18N
+//
+// org.jdesktop.layout.GroupLayout titlePanelLayout = new
org.jdesktop.layout.GroupLayout(
+// titlePanel);
+// titlePanel.setLayout(titlePanelLayout);
+// titlePanelLayout.setHorizontalGroup(titlePanelLayout
+//
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+// .add(titleIconLabel,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE, 461,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE));
+//
titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING).add(titleIconLabel));
+//
+// datasourceLabel.setFont(new java.awt.Font("SansSerif", 0, 12));
+// datasourceLabel.setText("Data Source");
+//
+// datasourceComboBox
+// .addActionListener(new
java.awt.event.ActionListener() {
+// public void
actionPerformed(java.awt.event.ActionEvent evt) {
+//
datasourceComboBoxActionPerformed(evt);
+// }
+// });
+//
+// aboutButton.setText("About");
+// aboutButton.setMargin(new java.awt.Insets(2, 5, 2, 5));
+// aboutButton.addActionListener(new
java.awt.event.ActionListener() {
+// public void actionPerformed(java.awt.event.ActionEvent
evt) {
+// aboutButtonActionPerformed(evt);
+// }
+// });
+//
+// org.jdesktop.layout.GroupLayout datasourcePanelLayout = new
org.jdesktop.layout.GroupLayout(
+// datasourcePanel);
+// datasourcePanel.setLayout(datasourcePanelLayout);
+// datasourcePanelLayout
+// .setHorizontalGroup(datasourcePanelLayout
+// .createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING)
+// .add(
+//
datasourcePanelLayout
+//
.createSequentialGroup()
+//
.addContainerGap()
+//
.add(datasourceLabel)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED)
+//
.add(datasourceComboBox, 0, 301,
+//
Short.MAX_VALUE)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED)
+//
.add(aboutButton).addContainerGap()));
+// datasourcePanelLayout
+// .setVerticalGroup(datasourcePanelLayout
+// .createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING)
+// .add(
+//
datasourcePanelLayout
+//
.createSequentialGroup()
+//
.addContainerGap()
+//
.add(
+//
datasourcePanelLayout
+//
.createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.BASELINE)
+//
.add(datasourceLabel)
+//
.add(aboutButton)
+//
.add(
+//
datasourceComboBox,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE))
+//
.addContainerGap(
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
Short.MAX_VALUE)));
+//
+//
buttonPanel.setBorder(javax.swing.BorderFactory.createEtchedBorder());
+//
+// searchButton.setText("Search");
+// searchButton.addActionListener(new
java.awt.event.ActionListener() {
+// public void actionPerformed(java.awt.event.ActionEvent
evt) {
+// searchButtonActionPerformed(evt);
+// }
+// });
+//
+// cancelButton.setText("Cancel");
+// cancelButton.addActionListener(new
java.awt.event.ActionListener() {
+// public void actionPerformed(java.awt.event.ActionEvent
evt) {
+// cancelButtonActionPerformed(evt);
+// }
+// });
+//
+// clearButton.setText("Clear");
+// clearButton.addActionListener(new
java.awt.event.ActionListener() {
+// public void actionPerformed(java.awt.event.ActionEvent
evt) {
+// clearButtonActionPerformed(evt);
+// }
+// });
+//
+// org.jdesktop.layout.GroupLayout buttonPanelLayout = new
org.jdesktop.layout.GroupLayout(
+// buttonPanel);
+// buttonPanel.setLayout(buttonPanelLayout);
+// buttonPanelLayout
+// .setHorizontalGroup(buttonPanelLayout
+// .createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING)
+// .add(
+//
org.jdesktop.layout.GroupLayout.TRAILING,
+//
buttonPanelLayout
+//
.createSequentialGroup()
+//
.addContainerGap()
+//
.add(clearButton)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED,
+//
225, Short.MAX_VALUE)
+//
.add(cancelButton)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED)
+//
.add(searchButton).addContainerGap()));
+// buttonPanelLayout
+// .setVerticalGroup(buttonPanelLayout
+// .createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING)
+// .add(
+//
org.jdesktop.layout.GroupLayout.TRAILING,
+//
buttonPanelLayout
+//
.createSequentialGroup()
+//
.addContainerGap(
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
Short.MAX_VALUE)
+//
.add(
+//
buttonPanelLayout
+//
.createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.BASELINE)
+//
.add(searchButton).add(
+//
cancelButton)
+//
.add(clearButton))
+//
.addContainerGap()));
+//
+// org.jdesktop.layout.GroupLayout dataQueryPanelLayout = new
org.jdesktop.layout.GroupLayout(
+// dataQueryPanel);
+// dataQueryPanel.setLayout(dataQueryPanelLayout);
+// dataQueryPanelLayout.setHorizontalGroup(dataQueryPanelLayout
+//
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+// .add(0, 461, Short.MAX_VALUE));
+// dataQueryPanelLayout.setVerticalGroup(dataQueryPanelLayout
+//
.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+// .add(0, 247, Short.MAX_VALUE));
+//
+// queryPanel = new JPanel();
+// org.jdesktop.layout.GroupLayout layout = new
org.jdesktop.layout.GroupLayout(
+// queryPanel);
+// queryPanel.setLayout(layout);
+// layout.setHorizontalGroup(layout.createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING).add(titlePanel,
+// org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+// org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
+// .add(datasourcePanel,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
Short.MAX_VALUE).add(buttonPanel,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
Short.MAX_VALUE).add(dataQueryPanel,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+// Short.MAX_VALUE));
+// layout
+// .setVerticalGroup(layout
+// .createParallelGroup(
+//
org.jdesktop.layout.GroupLayout.LEADING)
+// .add(
+// layout
+//
.createSequentialGroup()
+//
.add(
+//
titlePanel,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED)
+//
.add(
+//
datasourcePanel,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED)
+//
.add(
+//
dataQueryPanel,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
Short.MAX_VALUE)
+//
.addPreferredGap(
+//
org.jdesktop.layout.LayoutStyle.RELATED)
+//
.add(
+//
buttonPanel,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+//
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+//
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)));
+//
+// dataQueryPanel.setLayout(new BorderLayout());
+// createInstallPanel();
+// } // </editor-fold>
+//
+// private void createInstallPanel() {
+// installPanel = new JPanel();
+// installPanel.setLayout(new BorderLayout());
+// JLabel titleIconLabel2 = new JLabel();
+// titleIconLabel2.setIcon(new ImageIcon(Cytoscape.class
+// .getResource("images/networkImportIcon.png")));
+// JPanel titlePanel2 = new JPanel();
+// titlePanel2.add(titleIconLabel2);
+// titlePanel2.setBackground(new Color(0, 0, 0));
+// titlePanel2.setLayout(new FlowLayout(FlowLayout.LEFT));
+// if (numClients == 0) {
+// installPanel.add(titlePanel2, BorderLayout.NORTH);
+// }
+//
+// JPanel internalPanel = new JPanel();
+// internalPanel.setBorder(new EmptyBorder(10, 10, 10, 10));
+// internalPanel.setLayout(new BoxLayout(internalPanel,
+// BoxLayout.PAGE_AXIS));
+// JTextArea area = new JTextArea(1, 40);
+// area.setBorder(new EmptyBorder(0, 0, 0, 0));
+// if (numClients == 0) {
+// area
+// .setText("There are no network import
web service clients installed.");
+// } else {
+// area.setText("To install additional web service
clients, click the install button below.");
+// }
+// area.setEditable(false);
+// area.setOpaque(false);
+// area.setAlignmentX(Component.LEFT_ALIGNMENT);
+// internalPanel.add(area);
+// }
+//
+//
+// private void searchButtonActionPerformed(final ActionEvent evt) {
+// selectedClientID = clientNames
+// .get(datasourceComboBox.getSelectedItem());
+//
+// final CyWebServiceEvent<String> event = buildEvent();
+// logger.info("Start importing network: " +
evt.getActionCommand());
+//
+// task = new
WSNetworkImportTask(datasourceComboBox.getSelectedItem()
+// .toString(), event);
+//
+// // Configure JTask Dialog Pop-Up Box
+// final JTaskConfig tConfig = new JTaskConfig();
+// tConfig.setOwner(Cytoscape.getDesktop());
+// tConfig.displayCloseButton(true);
+// tConfig.displayCancelButton(true);
+// tConfig.displayStatus(false);
+// tConfig.setAutoDispose(true);
+//
+// // Execute Task in New Thread; pops open JTask Dialog Box.
+// TaskManager.executeTask(task, tConfig);
+//
+// logger.info("Network Import from WS Success!");
+// }
+//
+// private void aboutButtonActionPerformed(ActionEvent evt) {
+// final WebServiceClient<?> wsc = WebServiceClientManager
+// .getClient(selectedClientID);
+// final String clientName = wsc.getDisplayName();
+// final String description = wsc.getDescription();
+// Icon icon = null;
+// if (wsc instanceof WebServiceClientGUI) {
+// icon = ((WebServiceClientGUI)
wsc).getIcon(IconSize.FULL);
+// }
+//
+// if (icon == null) {
+// icon = DEF_ICON;
+// }
+// AboutDialog.showDialog(clientName, icon, description);
+// }
+//
+// /**
+// * Clear query text field.
+// */
+// private void clearButtonActionPerformed(java.awt.event.ActionEvent evt)
{
+// // Just set empty string for the field.
+// queryTextPane.setText("");
+// }
+//
+// private void cancelButtonActionPerformed(java.awt.event.ActionEvent
evt) {
+// // Do nothing. Just hide this window.
+// queryTextPane.setText("");
+// dispose();
+// }
+//
+// private void datasourceComboBoxActionPerformed(
+// java.awt.event.ActionEvent evt) {
+//
+// queryTextPane.setText("");
+//
setProperty(clientNames.get(datasourceComboBox.getSelectedItem()));
+// selectedClientID = clientNames
+// .get(datasourceComboBox.getSelectedItem());
+//
+// // Update Panel
+// dataQueryPanel.removeAll();
+//
+// final Container gui = serviceUIPanels.get(selectedClientID);
+// if (gui != null) {
+// // This service has custom panel.
+// dataQueryPanel.add(gui, BorderLayout.CENTER);
+// // Hide button panel.
+// buttonPanel.setVisible(false);
+// } else {
+// // Otherwise, use the default panel.
+// logger.info("No custom GUI. Use default panel.");
+// dataQueryPanel.add(mainTabbedPane, BorderLayout.CENTER);
+// buttonPanel.setVisible(true);
+// }
+//
+// pack();
+// repaint();
+// }
+//
+// private void setProperty(String clientID) {
+// final WebServiceClient<?> client =
WebServiceClientManager.getClient(clientID);
+//
+// if (client == null)
+// return;
+//
+// ModuleProperties props = client.getProps();
+// List<Tunable> tunables = props.getTunables();
+// propertyPanel = new JPanel(new GridLayout(0, 1));
+//
+// for (Tunable tu : tunables) {
+// JPanel p = tu.getPanel();
+// p.setBackground(Color.white);
+//
+// if (p != null)
+// propertyPanel.add(p);
+// }
+//
+// propertyScrollPane.setViewportView(propertyPanel);
+// pack();
+// repaint();
+// }
+//
+// private void setDatasource() {
+// List<WebServiceClient<?>> clients = WebServiceClientManager
+// .getAllClients();
+// for (WebServiceClient<?> client : clients) {
+// if (client instanceof NetworkImportWebServiceClient) {
+//
this.datasourceComboBox.addItem(client.getDisplayName());
+// this.clientNames.put(client.getDisplayName(),
client
+// .getClientID());
+//
+// if (client instanceof WebServiceClientGUI
+// && (((WebServiceClientGUI)
client).getGUI() != null)) {
+//
serviceUIPanels.put(client.getClientID(),
+// ((WebServiceClientGUI)
client).getGUI());
+// }
+// numDataSources++;
+// }
+// }
+// }
+//
+// private CyWebServiceEvent<String> buildEvent() {
+// final String clientID = clientNames.get(datasourceComboBox
+// .getSelectedItem());
+//
+// // Update props here.
+//
WebServiceClientManager.getClient(clientID).getProps().updateValues();
+//
+// return new CyWebServiceEvent<String>(clientID,
+// WSEventType.SEARCH_DATABASE,
queryTextPane.getText(),
+// WSEventType.IMPORT_NETWORK);
+// }
+//
+// // Variables declaration - do not modify
+// private javax.swing.JButton cancelButton;
+// private javax.swing.JComboBox datasourceComboBox;
+// private javax.swing.JLabel datasourceLabel;
+// private javax.swing.JTabbedPane mainTabbedPane;
+// private javax.swing.JPanel propertyPanel;
+// private JScrollPane propertyScrollPane;
+// private javax.swing.JButton searchButton;
+// private javax.swing.JScrollPane searchTermScrollPane;
+// private javax.swing.JTextPane queryTextPane;
+// private javax.swing.JButton aboutButton;
+// private javax.swing.JPanel buttonPanel;
+// private JPanel queryPanel;
+// private JPanel installPanel;
+// private javax.swing.JButton clearButton;
+// private javax.swing.JPanel dataQueryPanel;
+// private javax.swing.JPanel datasourcePanel;
+// private javax.swing.JLabel titleIconLabel;
+// private javax.swing.JPanel titlePanel;
+//
+//
+// /**
+// * Task to import network from web service.
+// *
+// * @author kono
+// *
+// */
+// private class WSNetworkImportTask implements Task {
+// private String serviceName;
+// private CyWebServiceEvent<String> evt;
+// private TaskMonitor taskMonitor;
+//
+// public WSNetworkImportTask(final String serviceName,
+// final CyWebServiceEvent<String> evt) {
+// this.evt = evt;
+// this.serviceName = serviceName;
+// }
+//
+// public String getTitle() {
+// return "Loading network from web service...";
+// }
+//
+// public void halt() {
+//
+// cancelFlag = true;
+// Thread.currentThread().interrupt();
+// taskMonitor.setPercentCompleted(100);
+//
+// // Kill the import task.
+// CyWebServiceEvent<String> cancelEvent = new
CyWebServiceEvent<String>(
+// serviceName, WSEventType.CANCEL, null,
null);
+// try {
+//
WebServiceClientManager.getCyWebServiceEventSupport()
+//
.fireCyWebServiceEvent(cancelEvent);
+// } catch (CyWebServiceException e) {
+// taskMonitor.setException(e, "Cancel Failed.");
+// }
+// }
+//
+// public void run() {
+// cancelFlag = false;
+// taskMonitor.setStatus("Loading network from " +
serviceName);
+// taskMonitor.setPercentCompleted(-1);
+//
+// try {
+//
WebServiceClientManager.getCyWebServiceEventSupport()
+// .fireCyWebServiceEvent(evt);
+// } catch (Exception e) {
+// taskMonitor.setException(e,
+// "Failed to load network from
web service.");
+// return;
+// }
+// taskMonitor.setPercentCompleted(100);
+// taskMonitor.setStatus("Network successfully loaded.");
+// }
+//
+// public void setTaskMonitor(TaskMonitor arg0)
+// throws IllegalThreadStateException {
+// this.taskMonitor = arg0;
+// }
+//
+// protected TaskMonitor getTaskMonitor() {
+// return taskMonitor;
+// }
+// }
+//
+// /**
+// * Listening to events fired by service clients.
+// *
+// * @param evt
+// * DOCUMENT ME!
+// */
+// public void propertyChange(PropertyChangeEvent evt) {
+//
+// if (cancelFlag)
+// return;
+//
+// Object resultObject = evt.getNewValue();
+//
+// if (evt.getPropertyName().equals(
+// WSResponseType.SEARCH_FINISHED.toString())
+// && (resultObject != null)
+// && resultObject instanceof
DatabaseSearchResult) {
+// DatabaseSearchResult result = (DatabaseSearchResult)
resultObject;
+//
+// if
(result.getNextMove().equals(WSEventType.IMPORT_NETWORK)) {
+// logger.info("Got search result from: " +
evt.getSource()
+// + ", Num result = " +
result.getResultSize()
+// + ", Source name = " +
evt.getOldValue());
+//
+// String[] message = {
+// result.getResultSize() + "
records found in "
+// +
selectedClientID,
+// "Do you want to create new
network from the search result?" };
+// int value =
JOptionPane.showConfirmDialog(Cytoscape
+// .getDesktop(), message, "Import
network",
+// JOptionPane.YES_NO_OPTION);
+//
+// if (value == JOptionPane.YES_OPTION) {
+// CyWebServiceEvent<Object> evt2 = new
CyWebServiceEvent<Object>(
+//
evt.getOldValue().toString(),
+//
WSEventType.IMPORT_NETWORK, result.getResult());
+//
+// try {
+//
WebServiceClientManager.getCyWebServiceEventSupport()
+//
.fireCyWebServiceEvent(evt2);
+// } catch (CyWebServiceException e) {
+// // TODO Auto-generated catch
block
+// if (task.getTaskMonitor() !=
null) {
+//
task.getTaskMonitor().setException(e,
+//
"Database search failed.");
+// }
+// }
+// }
+// }
+// } else if (evt.getPropertyName().equals(
+//
WSResponseType.DATA_IMPORT_FINISHED.toString())) {
+//
+// // If result is empty, just ignore it.
+// if (evt.getNewValue() == null)
+// return;
+//
+//// VisualStyle style = ((NetworkImportWebServiceClient)
WebServiceClientManager
+////
.getClient(selectedClientID)).getDefaultVisualStyle();
+//// if (style == null) {
+//// style =
Cytoscape.getVisualMappingManager().getVisualStyle();
+//// }
+////
+//// if
(Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+//// .getVisualStyle(style.getName()) ==
null)
+////
Cytoscape.getVisualMappingManager().getCalculatorCatalog()
+//// .addVisualStyle(style);
+////
+////
Cytoscape.getVisualMappingManager().setVisualStyle(style);
+//
+// // Name the network
+// final String[] message = { "Network Loaded from " +
selectedClientID,
+// "Please enter title for new network:" };
+// String value =
JOptionPane.showInputDialog(Cytoscape.getDesktop(),
+// message, "Name new network",
JOptionPane.QUESTION_MESSAGE);
+// if (value == null || value.length() == 0)
+// value = selectedClientID + " Network";
+//
+// final CyNetwork cyNetwork =
Cytoscape.getCurrentNetwork();
+// Cytoscape.getCurrentNetwork().setTitle(value);
+//
Cytoscape.getDesktop().getNetworkPanel().updateTitle(cyNetwork);
+// }
+// }
+}
Added:
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenu.java
===================================================================
---
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenu.java
(rev 0)
+++
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenu.java
2011-01-20 01:13:00 UTC (rev 23523)
@@ -0,0 +1,7 @@
+package org.cytoscape.webservice.internal.ui;
+
+public interface WebServiceContextMenu {
+ String getCategory();
+
+
+}
Added:
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
===================================================================
---
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
(rev 0)
+++
core3/webservice-impl/trunk/src/main/java/org/cytoscape/webservice/internal/ui/WebServiceContextMenuManager.java
2011-01-20 01:13:00 UTC (rev 23523)
@@ -0,0 +1,125 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package org.cytoscape.webservice.internal.ui;
+
+import javax.swing.JMenu;
+import javax.swing.JPopupMenu;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.view.model.View;
+
+
+/**
+ * Context menu for web service clients.
+ *
+ */
+public class WebServiceContextMenuManager {
+
+ private JMenu nodeRootMenu;
+ private JMenu edgeRootMenu;
+
+ /**
+ * Creates a new WebServiceContextMenu object.
+ */
+ public WebServiceContextMenuManager() {
+ nodeRootMenu = new JMenu("Use Web Services");
+ edgeRootMenu = new JMenu("Use Web Services");
+ }
+
+ /**
+ * Add this menu to the node context menu.
+ *
+ * @param nodeView DOCUMENT ME!
+ * @param menu DOCUMENT ME!
+ */
+ public void addNodeContextMenuItems(View<CyNode> nodeView, JPopupMenu
menu) {
+ addMenu(nodeView, menu);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param edgeView DOCUMENT ME!
+ * @param menu DOCUMENT ME!
+ */
+ public void addEdgeContextMenuItems(View<CyEdge> edgeView, JPopupMenu
menu) {
+ addMenu(edgeView, menu);
+ }
+
+ private void addMenu(View<? extends CyTableEntry> view, JPopupMenu
menu) {
+ if (menu == null)
+ menu = new JPopupMenu();
+ else {
+ // Clean up menu
+ nodeRootMenu.removeAll();
+ edgeRootMenu.removeAll();
+ }
+
+// List<JMenuItem> context = null;
+// final List<WebServiceClient<?>> clients =
WebServiceClientManager.getAllClients();
+//
+// for (WebServiceClient<?> client : clients) {
+// if (client instanceof WebServiceClientGUI) {
+// if (view.getModel() instanceof CyNode)
+// context = ((WebServiceClientGUI)
client).getNodeContextMenuItems((NodeView) view);
+// else if (view.getModel() instanceof CyEdge)
+// context = ((WebServiceClientGUI)
client).getEdgeContextMenuItems((EdgeView) view);
+//
+// if (context != null) {
+// JMenu cMenu = new
JMenu(client.getDisplayName());
+//
+// for (JMenuItem menuItem : context) {
+// cMenu.add(menuItem);
+// }
+//
+// nodeRootMenu.add(cMenu);
+// clientMap.put(client.getDisplayName(),
client.getClientID());
+// }
+// }
+// }
+//
+// if(view instanceof NodeView) {
+// menu.add(this.nodeRootMenu);
+// if(nodeRootMenu.getItemCount() == 0)
+// nodeRootMenu.setEnabled(false);
+// } else {
+// menu.add(this.edgeRootMenu);
+// if(edgeRootMenu.getItemCount() == 0)
+// edgeRootMenu.setEnabled(false);
+// }
+ }
+}
Modified:
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-20 01:12:41 UTC (rev 23522)
+++
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-01-20 01:13:00 UTC (rev 23523)
@@ -5,8 +5,5 @@
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
default-lazy-init="false">
-
- <osgi:service id="webServiceClientManagerService"
ref="webServiceClientManager">
- </osgi:service>
</beans>
Modified:
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-20 01:12:41 UTC (rev 23522)
+++
core3/webservice-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2011-01-20 01:13:00 UTC (rev 23523)
@@ -20,6 +20,5 @@
<context:annotation-config />
- <bean id="webServiceClientManager"
class="org.cytoscape.webservice.internal.WebServiceClientManagerImpl" />
</beans>
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