/*
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.bridgedb.cytoscape.internal.ui;
import org.bridgedb.cytoscape.internal.IDMapperClient;
import org.bridgedb.cytoscape.internal.util.DataSourceUtil;
import org.cytoscape.work.TaskMonitor;
//import cytoscape.task.ui.JTaskConfig;
import org.cytoscape.work.TaskManager;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Set;
import javax.swing.JOptionPane;
import javax.swing.event.TreeSelectionEvent;
import javax.swing.event.TreeSelectionListener;
import javax.swing.tree.TreePath;
import javax.swing.tree.DefaultMutableTreeNode;
import org.bridgedb.AttributeMapper;
import org.bridgedb.DataSource;
import org.bridgedb.IDMapper;
import org.bridgedb.IDMapperCapabilities;
import org.bridgedb.IDMapperException;
import org.bridgedb.Xref;
import org.cytoscape.util.swing.FileUtil;
import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
import org.bridgedb.cytoscape.internal.IDMapperClientManager;
/**
*
* @author gjj
*/
public class IDMappingSourceConfigDialog extends javax.swing.JDialog {
private final IDMapperClientManager idMapperClientManager;
public IDMappingSourceConfigDialog(javax.swing.JFrame parent,
TaskManager taskManager, OpenBrowser openBrowser,
FileUtil fileUtil, IDMapperClientManager idMapperClientManager,
boolean modal) {
super(parent, modal);
this.taskManager = taskManager;
this.openBrowser = openBrowser;
this.fileUtil = fileUtil;
this.idMapperClientManager = idMapperClientManager;
init();
}
public IDMappingSourceConfigDialog(javax.swing.JDialog parent,
TaskManager taskManager, OpenBrowser openBrowser,
FileUtil fileUtil, IDMapperClientManager idMapperClientManager,
boolean modal) {
super(parent, modal);
this.taskManager = taskManager;
this.openBrowser = openBrowser;
this.fileUtil = fileUtil;
this.idMapperClientManager = idMapperClientManager;
init();
}
@Deprecated
// for using window builder
public IDMappingSourceConfigDialog(TaskManager taskManager,
OpenBrowser openBrowser, FileUtil fileUtil,
IDMapperClientManager idMapperClientManager) {
this.taskManager = taskManager;
this.openBrowser = openBrowser;
this.fileUtil = fileUtil;
this.idMapperClientManager = idMapperClientManager;
init();
}
public void init() {
initComponents();
srcTree.addTreeSelectionListener(new TreeSelectionListener() {
/*
* on the select tree value changed. call this method to handle the event
* 2013-9-19:下午11:13:12<br>
*/
public void valueChanged(TreeSelectionEvent e) {
TreePath path = e.getPath();
if (path == null) {
descTextArea.setText(msg);
} else {
Object nodeObj = path.getLastPathComponent();
if (nodeObj instanceof DefaultMutableTreeNode) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode) nodeObj;
Object clientObj = node.getUserObject();
if (clientObj instanceof IDMapperClient) {
IDMapperClient client = (IDMapperClient) clientObj;
// final JTaskConfig jTaskConfig = new JTaskConfig();
// jTaskConfig.setOwner(cytoscape.Cytoscape.getDesktop());
// jTaskConfig.displayCloseButton(true);
// jTaskConfig.displayCancelButton(false);
// jTaskConfig.displayStatus(true);
// jTaskConfig.setAutoDispose(true);
// jTaskConfig.setMillisToPopup(100);
//
final LoadClientDescTask task = new LoadClientDescTask(client);
final TaskIterator ti = new TaskIterator(task);
taskManager.execute(ti);
} else {
descTextArea.setText(msg);
}
} else {
descTextArea.setText(msg);
}
}
descTextArea.repaint();
descScrollPane.repaint();
}
});
}
/**
* 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.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed"
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
java.awt.GridBagConstraints gridBagConstraints;
javax.swing.JPanel sourceConfPanel = new javax.swing.JPanel();
javax.swing.JSplitPane sourceDescSplitPane = new javax.swing.JSplitPane();
javax.swing.JScrollPane srcTreeScrollPane = new javax.swing.JScrollPane();
descScrollPane = new javax.swing.JScrollPane();
descTextArea = new javax.swing.JTextArea();
javax.swing.JPanel defaultPanel = new javax.swing.JPanel();
javax.swing.JButton loadDefaultButton = new javax.swing.JButton();
javax.swing.JButton saveAsDefaultButton = new javax.swing.JButton();
javax.swing.JPanel closePanel = new javax.swing.JPanel();
javax.swing.JButton closeButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("ID Mapping Source Configuration");
getContentPane().setLayout(new java.awt.GridBagLayout());
sourceConfPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("ID Mapping Resources Configuration"));
sourceConfPanel.setPreferredSize(new java.awt.Dimension(833, 542));
sourceConfPanel.setLayout(new java.awt.GridBagLayout());
sourceDescSplitPane.setDividerLocation(300);
sourceDescSplitPane.setPreferredSize(new java.awt.Dimension(800, 500));
srcTreeScrollPane.setMinimumSize(new java.awt.Dimension(200, 200));
srcTreeScrollPane.setPreferredSize(new java.awt.Dimension(300, 500));
srcTree = new IDMappingSourceSelectionTree(this, taskManager, openBrowser, fileUtil, idMapperClientManager);
srcTreeScrollPane.setViewportView(srcTree);
sourceDescSplitPane.setLeftComponent(srcTreeScrollPane);
descScrollPane.setPreferredSize(new java.awt.Dimension(500, 500));
descTextArea.setEditable(false);
descTextArea.setLineWrap(true);
descTextArea.setTabSize(4);
descTextArea.setText(msg);
descTextArea.setWrapStyleWord(true);
descScrollPane.setViewportView(descTextArea);
sourceDescSplitPane.setRightComponent(descScrollPane);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.weighty = 1.0;
gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
sourceConfPanel.add(sourceDescSplitPane, gridBagConstraints);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 0;
gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.weighty = 1.0;
gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
getContentPane().add(sourceConfPanel, gridBagConstraints);
defaultPanel.setVisible(false);
loadDefaultButton.setText("Load default resources");
loadDefaultButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadDefaultButtonActionPerformed(evt);
}
});
defaultPanel.add(loadDefaultButton);
saveAsDefaultButton.setText("Save current resources as default");
saveAsDefaultButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
saveAsDefaultButtonActionPerformed(evt);
}
});
defaultPanel.add(saveAsDefaultButton);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_START;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
getContentPane().add(defaultPanel, gridBagConstraints);
closePanel.setLayout(new javax.swing.BoxLayout(closePanel, javax.swing.BoxLayout.LINE_AXIS));
closeButton.setText("Close");
closeButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
closeButtonActionPerformed(evt);
}
});
closePanel.add(closeButton);
gridBagConstraints = new java.awt.GridBagConstraints();
gridBagConstraints.gridx = 0;
gridBagConstraints.gridy = 1;
gridBagConstraints.anchor = java.awt.GridBagConstraints.LINE_END;
gridBagConstraints.weightx = 1.0;
gridBagConstraints.insets = new java.awt.Insets(5, 5, 5, 5);
getContentPane().add(closePanel, gridBagConstraints);
pack();
}// </editor-fold>//GEN-END:initComponents
private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) {// GEN-FIRST:event_closeButtonActionPerformed
setVisible(false);
this.dispose();
try {
if (srcTree.isModified())
idMapperClientManager.saveCurrentToCytoscapeGlobalProperties();
} catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(this,
"Failed to save the current resources.");
}
}// GEN-LAST:event_closeButtonActionPerformed
private void saveAsDefaultButtonActionPerformed(java.awt.event.ActionEvent evt) {// GEN-FIRST:event_saveAsDefaultButtonActionPerformed
int ret = JOptionPane.showConfirmDialog(this,
"Are you sure to replace the default resources with"
+ " the current ones?", null, JOptionPane.YES_NO_OPTION);
if (ret == JOptionPane.NO_OPTION)
return;
try {
idMapperClientManager.saveCurrentToCytoscapeGlobalProperties();
} catch (Exception e) {
e.printStackTrace();
JOptionPane.showMessageDialog(this,
"Failed to save the current resources.");
}
JOptionPane.showMessageDialog(this,
"The current resources has been save as default.");
}// GEN-LAST:event_saveAsDefaultButtonActionPerformed
private void loadDefaultButtonActionPerformed(java.awt.event.ActionEvent evt) {// GEN-FIRST:event_loadDefaultButtonActionPerformed
int ret = JOptionPane.showConfirmDialog(this,
"Are you sure to load the default resources?\n"
+ "The current resources will be replaced with the default ones.",
null, JOptionPane.YES_NO_OPTION);
if (ret == JOptionPane.NO_OPTION)
return;
idMapperClientManager.reloadFromCytoscapeGlobalProperties();
srcTree.reset();
JOptionPane.showMessageDialog(this,
"The default resources has been loaded.");
}// GEN-LAST:event_loadDefaultButtonActionPerformed
public boolean isModified() {
return srcTree.isModified();
}
private static final String msg = "Click on a 2nd level tree node to "
+ "add an ID mapping sources.\n\nClick on a tree node of a ID "
+ "mapping source for information about it. \n\nRight click on a ID "
+ "mapping source to delete it.\n\nClick the checkboxes to "
+ "select/unselect ID mapping sources to use.";
private IDMappingSourceSelectionTree srcTree;
private final TaskManager taskManager;
private final OpenBrowser openBrowser;
private final FileUtil fileUtil;
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JScrollPane descScrollPane;
private javax.swing.JTextArea descTextArea;
// End of variables declaration//GEN-END:variables
private class LoadClientDescTask extends AbstractTask {
private final IDMapperClient client;
public LoadClientDescTask(final IDMapperClient client) {
this.client = client;
}
@Override
public void cancel() {
// cannot cancel
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
try {
taskMonitor.setStatusMessage("Connecting to " + client.getDisplayName()
+ "...");
taskMonitor.setProgress(0.00);
descTextArea.setText(getDescription());
taskMonitor.setStatusMessage("Done");
taskMonitor.setProgress(1.00);
} catch (Exception e) {
taskMonitor.setProgress(1.00);
taskMonitor.setStatusMessage("failed.\n");
e.printStackTrace();
descTextArea.setText("Failed to retrieve the information about this ID mapping client.");
}
}
private String getDescription() throws IDMapperException {
IDMapper idMapper = client.getIDMapper();
if (idMapper == null) {
return "This ID mapping client cannot be connected.";
}
StringBuilder desc = new StringBuilder(client.getDisplayName());
desc.append("\nCapacities:\n");
desc.append(">> Supported source ID types:\n");
IDMapperCapabilities capabilities = idMapper.getCapabilities();
Set<DataSource> dss = capabilities.getSupportedSrcDataSources();
if (dss != null) {
ArrayList<String> vec = new ArrayList(dss.size());
for (DataSource ds : dss) {
vec.add(getDescription(ds));
}
Collections.sort(vec);
for (String str : vec) {
desc.append("\t" + str + "\n");
}
}
desc.append(">> Supported target ID types:\n");
dss = capabilities.getSupportedTgtDataSources();
if (dss != null) {
ArrayList<String> vec = new ArrayList(dss.size());
int i = 0;
for (DataSource ds : dss) {
i++;
vec.add(getDescription(ds));
}
Collections.sort(vec);
for (String str : vec) {
desc.append("\t" + str + "\n");
}
}
// desc.append(">> Is free-text search supported?\n");
// desc.append(capabilities.isFreeSearchSupported()? "\tYes":"\tNo");
// desc.append("\n");
// TODO: remove next line after the problem of AttributeMapper in
// BridgeRest is solved.
// TODO: temporally comment the next line, I don't know that it is useful
// in 3.0, or not?
// Chao Zhang 2013-09-06
// if (!(idMapper instanceof
// org.bridgedb.webservice.bridgerest.BridgeRest))
if (idMapper instanceof AttributeMapper) {
desc.append(">>Supported Attributes\n");
Set<String> attrs = ((AttributeMapper) idMapper).getAttributeSet();
if (attrs != null) {
ArrayList<String> vec = new ArrayList(attrs.size());
int i = 0;
for (String attr : attrs) {
i++;
vec.add(attr);
}
Collections.sort(vec);
for (String str : vec) {
desc.append("\t" + str + "\n");
}
}
}
return desc.toString();
}
private String getDescription(DataSource dataSource) {
StringBuilder desc = new StringBuilder();
if (dataSource == null) {
System.err.print("wrong");
}
String sysName = dataSource.getSystemCode();
if (sysName != null) {
desc.append(sysName);
}
desc.append("\t");
String fullName = DataSourceUtil.getName(dataSource);
if (fullName != null) {
desc.append(fullName);
}
desc.append("\t");
Xref example = dataSource.getExample();
if (example != null) {
String id = example.getId();
if (id != null) {
desc.append(id);
}
}
return desc.toString();
}
}
}