/* File: PluginManageDialog.java Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org) 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 cytoscape.dialogs.plugins; import cytoscape.Cytoscape; import cytoscape.CytoscapeVersion; import cytoscape.bookmarks.Bookmarks; import cytoscape.bookmarks.DataSource; import cytoscape.dialogs.preferences.BookmarkDialog; import cytoscape.dialogs.preferences.EditBookmarkDialog; import cytoscape.logger.CyLogger; import cytoscape.plugin.DownloadableInfo; import cytoscape.plugin.ManagerUtil; import cytoscape.plugin.PluginInquireAction; import cytoscape.plugin.PluginManagerInquireTask; import cytoscape.plugin.PluginStatus; import cytoscape.plugin.ThemeInfo; import cytoscape.plugin.PluginInfo; import cytoscape.plugin.PluginManager; import cytoscape.plugin.PluginException; import cytoscape.plugin.ManagerException; import cytoscape.task.TaskMonitor; import cytoscape.task.ui.JTaskConfig; import cytoscape.task.util.TaskManager; import cytoscape.util.BookmarksUtil; import cytoscape.util.OpenBrowser; import java.awt.Component; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.util.List; import java.util.Map; import java.util.Vector; import javax.swing.*; import javax.swing.event.TreeSelectionEvent; import javax.swing.event.TreeSelectionListener; import javax.swing.tree.TreePath; import java.util.ArrayList; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; import java.awt.Color; import javax.swing.event.ListSelectionEvent; import javax.swing.event.ListSelectionListener; public class PluginManageDialog extends javax.swing.JDialog implements TreeSelectionListener, ActionListener { private static CyLogger logger = CyLogger.getLogger(PluginManageDialog.class); public static String CURRENTLY_INSTALLED = "Currently Installed"; public static String AVAILABLE_FOR_INSTALL = "Available for Install"; public static String defaultPluginSiteUrl = cytoscape.CytoscapeInit.getProperties().getProperty("defaultPluginDownloadUrl"); public static String DefaultPluginSiteTitle = "Cytoscape"; //private boolean hasPluginSiteURLChanged = false; private String currentPluginSiteURL = defaultPluginSiteUrl; private String HOWTOSEARCH = "You can use wildcard * or ? in your search words"; public enum PluginInstallStatus { INSTALLED(CURRENTLY_INSTALLED), AVAILABLE(AVAILABLE_FOR_INSTALL); private String typeText; private PluginInstallStatus(String type) { typeText = type; } public String toString() { return typeText; } } public enum CommonError { NOXML("ERROR: Failed to read XML file "), BADXML( "ERROR: XML file may be incorrectly formatted, unable to read "); private String errorText; private CommonError(String error) { errorText = error; } public String toString() { return errorText; } } private String baseSiteLabel = "Plugins available for download from: "; public PluginManageDialog() { this.setTitle("Manage Plugins"); initComponents(); initTree(); this.setSize(600, 500); } public PluginManageDialog(javax.swing.JDialog owner) { super(owner, "Manage Plugins"); setLocationRelativeTo(owner); initComponents(); initTree(); this.setSize(600, 500); } public PluginManageDialog(javax.swing.JFrame owner) { super(owner, "Manage Plugins"); setLocationRelativeTo(owner); initComponents(); initTree(); this.setSize(600, 500); this.btnSearch.setEnabled(false); this.availablePluginsLabel.setVisible(false); this.downloadLocText.setVisible(false); //this.sitePanel2.setVisible(false); //this.changeSiteButton.setVisible(false); this.btnClear.setEnabled(false); bookmarksSetUp(); this.lstDownloadSites.setCellRenderer(new BookmarkCellRenderer()); this.lstDownloadSites.addListSelectionListener(new MyListSelectionListener()); this.lstDownloadSites.getSelectionModel().setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION); loadBookmarkCMBox(true); //this.lbSiteURL.setText(((DataSource)this.cmbDownloadSites.getSelectedItem()).getHref()); //this.jTabbedPane1.setSelectedIndex(1); this.jTabbedPane1.addChangeListener(new MyChangeListener()); this.tfSearch.setToolTipText(HOWTOSEARCH); // by default, show all the plugins this.versionCheck.setSelected(false); this.btnEditSite.setEnabled(false); this.btnDeleteSite.setEnabled(false); } class MyChangeListener implements ChangeListener { public void stateChanged(ChangeEvent e){ int width = PluginManageDialog.this.jTabbedPane1.getSize().width; if (PluginManageDialog.this.jTabbedPane1.getSelectedIndex() == 0){ //PluginManageDialog.this.jTabbedPane1.setMinimumSize(new Dimension(width, 50)); //PluginManageDialog.this.jTabbedPane1.setPreferredSize(new Dimension(width, 50)); //PluginManageDialog.this.pnlSearch.setPreferredSize(new Dimension(width, 50)); //PluginManageDialog.this.pnlSettings.setPreferredSize(new Dimension(width, 50)); } else { //PluginManageDialog.this.jTabbedPane1.setMinimumSize(new Dimension(width, 150)); //PluginManageDialog.this.jTabbedPane1.setPreferredSize(new Dimension(width, 150)); //PluginManageDialog.this.pnlSearch.setPreferredSize(new Dimension(width, 150)); //PluginManageDialog.this.pnlSettings.setPreferredSize(new Dimension(width, 150)); } //PluginManageDialog.this.pack(); } } // Refresh the plugin-tree after the change of Plugin site URL private void refreshPluginTree(){ switchDownloadSites(); cytoscape.task.Task task = new PluginManagerInquireTask (this.currentPluginSiteURL, new UrlAction(this, this.currentPluginSiteURL)); // Configure JTask Dialog Pop-Up Box JTaskConfig jTaskConfig = new JTaskConfig(); jTaskConfig.setOwner(Cytoscape.getDesktop()); jTaskConfig.displayCloseButton(false); jTaskConfig.displayStatus(true); jTaskConfig.setAutoDispose(true); jTaskConfig.displayCancelButton(true); // Execute Task in New Thread; pop open JTask Dialog Box. TaskManager.executeTask(task, jTaskConfig); } private class UrlAction extends PluginInquireAction { private PluginManageDialog dialog; private String url; public UrlAction(PluginManageDialog Dialog, String Url) { dialog = Dialog; url = Url; } public boolean displayProgressBar() { return true; } public String getProgressBarMessage() { return "Attempting to connect..."; } public void inquireAction(List Results) { if (isExceptionThrown()) { if (getIOException() != null) { // failed to read the given url logger.warn(PluginManageDialog.CommonError.NOXML + url, getIOException()); dialog.setError(PluginManageDialog.CommonError.NOXML + url); } else if (getJDOMException() != null) { // failed to parse the xml file at the url logger.warn(PluginManageDialog.CommonError.BADXML + url, getJDOMException()); dialog.setError(PluginManageDialog.CommonError.BADXML + url); } } else { PluginManager Mgr = PluginManager.getPluginManager(); List UniqueAvailable = ManagerUtil.getUnique(Mgr .getDownloadables(PluginStatus.CURRENT), Results); Map> NewPlugins = ManagerUtil .sortByCategory(UniqueAvailable); if (NewPlugins.size() <= 0) { dialog.setError("No plugins compatible with " + new CytoscapeVersion().getFullVersion() + " available from this site."); } else { dialog.setMessage(""); } for (String Category : NewPlugins.keySet()) { dialog.addCategory(Category, NewPlugins.get(Category), PluginManageDialog.PluginInstallStatus.AVAILABLE); } } } } // trying to listen to events in the Url dialog public void actionPerformed(ActionEvent evt) { logger.info("URL DIALOG: " + evt.getSource().toString()); } /** * Enables the delete/install buttons when the correct leaf node is selected */ public void valueChanged(TreeSelectionEvent e) { TreeNode Node = (TreeNode) pluginTree.getLastSelectedPathComponent(); if (Node == null) { return; } if (Node.isLeaf()) { // display any object selected infoTextPane.setContentType("text/html"); infoTextPane.setText(((DownloadableInfo) Node.getObject()).htmlOutput()); infoTextPane.setCaretPosition(0); infoTextPane.setEditable(false); infoTextPane.addHyperlinkListener(new javax.swing.event.HyperlinkListener() { public void hyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) { if (evt.getEventType() == javax.swing.event.HyperlinkEvent.EventType.ACTIVATED) { // call open browser on the link OpenBrowser.openURL(evt.getURL().toString()); } } }); if (Node.getParent().getParent().getTitle().equalsIgnoreCase(CURRENTLY_INSTALLED)) { installDeleteButton.setText("Delete"); if (PluginManager.usingWebstartManager()) { installDeleteButton.setEnabled(false); setMessage("Delete is unavailable when using Web Start"); } else { installDeleteButton.setEnabled(true); } } else if (Node.getParent().getParent().getTitle().equalsIgnoreCase(AVAILABLE_FOR_INSTALL)) { installDeleteButton.setText("Install"); installDeleteButton.setEnabled(true); } } else { installDeleteButton.setEnabled(false); } } /** * Sets a message to be shown to the user regarding the plugin management * actions. * * @param Msg */ public void setMessage(String Msg) { msgPanel.setForeground(java.awt.Color.BLACK); msgPanel.setText(Msg); } public void setError(String Msg) { msgPanel.setForeground(new java.awt.Color(204, 0, 51)); msgPanel.setText(Msg); } /** * Set the name of the site the available plugins are from. * * @param SiteName */ public void setSiteName(String SiteName) { downloadLocText.setText(SiteName); } /** * Call this when changing download sites to clear out the old available * list in order to create a new one. */ public void switchDownloadSites() { hiddenNodes.clear(); java.util.Vector AvailableNodes = new java.util.Vector( availableNode.getChildren()); for (TreeNode child : AvailableNodes) { treeModel.removeNodeFromParent(child); } } /** * Adds a category and it's list of plugins to the appropriate tree (based * on Status) in the dialog. * * @param CategoryName * String category for this list of plugins * @param Plugins * List of DownloadableInfo objects to be shown in the given * category * @param Status * PluginInstallStatus (currently installed or available for * install) */ public void addCategory(String CategoryName, List Plugins, PluginInstallStatus Status) { switch (Status) { case INSTALLED: addCategory(CategoryName, Plugins, installedNode); break; case AVAILABLE: addCategory(CategoryName, Plugins, availableNode); if (treeModel.getIndexOfChild(rootTreeNode, availableNode) < 0) { treeModel.addNodeToParent(rootTreeNode, availableNode); } break; } javax.swing.ToolTipManager.sharedInstance().registerComponent( pluginTree); javax.swing.ImageIcon warningIcon = createImageIcon( "/cytoscape/images/misc/alert-red2.gif", "Warning"); javax.swing.ImageIcon okIcon = createImageIcon( "/cytoscape/images/misc/check-mark.gif", "Ok"); if (warningIcon != null) { treeRenderer = new TreeCellRenderer(warningIcon, okIcon); pluginTree.setCellRenderer(treeRenderer); } pluginTree.expandPath( new TreePath(availableNode.getPath()) ); pluginTree.expandPath( new TreePath(installedNode.getPath()) ); } // add category to the set of plugins under given node private void addCategory(String CategoryName, List Plugins, TreeNode node) { TreeNode Category = new TreeNode(CategoryName, true); for (DownloadableInfo CurrentPlugin : Plugins) { TreeNode PluginNode = new TreeNode(CurrentPlugin); if (node.equals(availableNode) && !CurrentPlugin.isPluginCompatibleWithCurrent()) { java.util.List hiddenCat = hiddenNodes.get(Category); if (hiddenCat == null) hiddenCat = new java.util.ArrayList(); hiddenCat.add(PluginNode); hiddenNodes.put(Category, hiddenCat); if (!versionCheck.isSelected()) treeModel.addNodeToParent(Category, PluginNode); } else { treeModel.addNodeToParent(Category, PluginNode); } } if (Category.getChildCount() > 0) treeModel.addNodeToParent(node, Category); } // allow for outdated versions private void versionCheckItemStateChanged(java.awt.event.ItemEvent evt) { TreePath[] SelectedPaths = pluginTree.getSelectionPaths(); if (evt.getStateChange() == ItemEvent.DESELECTED) { pluginTree.collapsePath( new TreePath(availableNode.getPath()) ); availableNode.removeChildren(); for (TreeNode Category : hiddenNodes.keySet()) { for (TreeNode Plugin : hiddenNodes.get(Category)) { treeModel.addNodeToParent(Category, Plugin); } treeModel.addNodeToParent(availableNode, Category); } } else if (evt.getStateChange() == ItemEvent.SELECTED) { for (TreeNode Category : hiddenNodes.keySet()) { for (TreeNode Plugin: hiddenNodes.get(Category)) { hiddenNodes.get(Category); treeModel.removeNodesFromParent(hiddenNodes.get(Category)); if (Category.getChildCount() <= 0) { availableNode.removeChild(Category); treeModel.reload(); } } } } if (SelectedPaths != null) { for (TreePath Path: SelectedPaths) { pluginTree.expandPath(Path); pluginTree.setSelectionPath(Path); } } else { pluginTree.expandPath( new TreePath(availableNode.getPath()) ); pluginTree.expandPath( new TreePath(installedNode.getPath()) ); } } private void installDeleteButtonActionPerformed(ActionEvent evt) { if (installDeleteButton.getText().equals("Delete")) { deleteButtonActionPerformed(evt); } else if (installDeleteButton.getText().equals("Install")) { installButtonActionPerformed(evt); } } // delete event private void deleteButtonActionPerformed(ActionEvent evt) { TreeNode Node = (TreeNode) pluginTree.getLastSelectedPathComponent(); if (Node == null) { return; } DownloadableInfo NodeInfo = Node.getObject(); String ChangeMsg = "Changes will not take effect until you have restarted Cytoscape."; String VerifyMsg = ""; if (NodeInfo.getCategory().equalsIgnoreCase("core")) { VerifyMsg = "This is a 'core' plugin and other plugins may depend on it, " + "are you sure you want to delete it?\n" + ChangeMsg; } else { VerifyMsg = "Are you sure you want to delete the plugin '" + NodeInfo.getName() + "'?\n" + ChangeMsg; } if (JOptionPane.YES_OPTION == JOptionPane.showConfirmDialog(this, VerifyMsg, "Verify Delete Plugin", JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE)) { try { PluginManager.getPluginManager().delete(NodeInfo); treeModel.removeNodeFromParent(Node); setMessage(NodeInfo.getName() + " will be removed when you restart Cytoscape."); } catch (cytoscape.plugin.WebstartException we) { logger.warn("Unable to remove '"+NodeInfo.getName()+"': "+we.getMessage(), we); } } } // install new downloadable obj private void installButtonActionPerformed(java.awt.event.ActionEvent evt) { final TreeNode node = (TreeNode) pluginTree .getLastSelectedPathComponent(); if (node == null) { // error return; } Object nodeInfo = node.getObject(); if (node.isLeaf()) { boolean licenseRequired = false; final LicenseDialog License = new LicenseDialog(this); final DownloadableInfo infoObj = (DownloadableInfo) nodeInfo; switch (infoObj.getType()) { case PLUGIN: if (infoObj.getLicenseText() != null) { License.addPlugin(infoObj); licenseRequired = true; } break; case THEME: ThemeInfo themeInfo = (ThemeInfo) infoObj; for (PluginInfo pInfo : themeInfo.getPlugins()) { if (pInfo.getLicenseText() != null) { License.addPlugin(pInfo); licenseRequired = true; } } break; case FILE: // currently nothing, there are no FileInfo objects // right now break; } if (licenseRequired) { License.addListenerToOk(new ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { License.dispose(); createInstallTask(infoObj, node); } }); License.selectDefault(); License.setVisible(true); } else { createInstallTask(infoObj, node); } } } private void updateCurrent(DownloadableInfo info) { boolean categoryMatched = false; for (TreeNode Child : installedNode.getChildren()) { if (Child.getTitle().equals(info.getCategory())) { Child.addChild(new TreeNode(info)); categoryMatched = true; } } if (!categoryMatched) { List NewPlugin = new java.util.ArrayList(); NewPlugin.add(info); addCategory(info.getCategory(), NewPlugin, PluginInstallStatus.INSTALLED); } } // close button private void closeButtonActionPerformed(java.awt.event.ActionEvent evt) { dispose(); } // initialize the JTree and base nodes private void initTree() { pluginTree.setRootVisible(false); pluginTree.addTreeSelectionListener(this); pluginTree.getSelectionModel().setSelectionMode( javax.swing.tree.TreeSelectionModel.SINGLE_TREE_SELECTION); rootTreeNode = new TreeNode("Plugins", true); installedNode = new TreeNode(PluginInstallStatus.INSTALLED.toString(), true); availableNode = new TreeNode(PluginInstallStatus.AVAILABLE.toString(), true); treeModel = new ManagerModel(rootTreeNode); treeModel.addNodeToParent(rootTreeNode, installedNode); treeModel.addNodeToParent(rootTreeNode, availableNode); pluginTree.setModel(treeModel); hiddenNodes = new java.util.HashMap>(); } private Vector getAllPluginVector(){ Vector allPluginVect = new Vector(); TreeNode root = (TreeNode) this.treeModel.getRoot(); for (int i=0; i< root.getChildCount(); i++){ TreeNode n = root.getChildAt(i); Vector categories = n.getChildren(); for (int j=0; j treeNodeVect = root.getChildren(); for (int i=0; i< treeNodeVect.size(); i++){ TreeNode n = treeNodeVect.elementAt(i); pluginTree.expandPath(new TreePath(treeModel.getPathToRoot(n))); } // switch the sitePanel this.sitePanel.setVisible(true); //this.sitePanel2.setVisible(false); } /** 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() { java.awt.GridBagConstraints gridBagConstraints; jSplitPane2 = new javax.swing.JSplitPane(); jTabbedPane1 = new javax.swing.JTabbedPane(); pnlSearch = new javax.swing.JPanel(); topPane = new javax.swing.JPanel(); sitePanel = new javax.swing.JPanel(); tfSearch = new javax.swing.JTextField(); btnSearch = new javax.swing.JButton(); btnClear = new javax.swing.JButton(); downloadLocText = new javax.swing.JLabel(); lbSearchTitle = new javax.swing.JLabel(); pnlSettings = new javax.swing.JPanel(); jLabel3 = new javax.swing.JLabel(); jPanel2 = new javax.swing.JPanel(); btnAddSite = new javax.swing.JButton(); btnEditSite = new javax.swing.JButton(); btnDeleteSite = new javax.swing.JButton(); jScrollPane1 = new javax.swing.JScrollPane(); lstDownloadSites = new javax.swing.JList(); jPanel3 = new javax.swing.JPanel(); availablePluginsLabel = new javax.swing.JLabel(); versionCheck = new javax.swing.JCheckBox(); jSplitPane1 = new javax.swing.JSplitPane(); treeScrollPane = new javax.swing.JScrollPane(); pluginTree = new javax.swing.JTree(); infoScrollPane = new javax.swing.JScrollPane(); infoTextPane = new javax.swing.JEditorPane(); msgLabel = new javax.swing.JLabel(); msgPanel = new javax.swing.JTextArea(); bottomPane = new javax.swing.JPanel(); buttonPanel = new javax.swing.JPanel(); installDeleteButton = new javax.swing.JButton(); closeButton = new javax.swing.JButton(); getContentPane().setLayout(new java.awt.GridBagLayout()); setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE); jSplitPane2.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT); pnlSearch.setLayout(new java.awt.GridBagLayout()); topPane.setLayout(new java.awt.GridBagLayout()); sitePanel.setLayout(new java.awt.GridBagLayout()); tfSearch.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { tfSearchActionPerformed(evt); } }); tfSearch.addKeyListener(new java.awt.event.KeyAdapter() { public void keyTyped(java.awt.event.KeyEvent evt) { tfSearchKeyTyped(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridy = 3; gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL; gridBagConstraints.weightx = 1.0; sitePanel.add(tfSearch, gridBagConstraints); btnSearch.setText("Search"); btnSearch.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { btnSearchActionPerformed(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 1; gridBagConstraints.gridy = 3; gridBagConstraints.insets = new java.awt.Insets(5, 10, 5, 10); sitePanel.add(btnSearch, gridBagConstraints); btnClear.setText("Clear"); btnClear.setPreferredSize(new java.awt.Dimension(67, 23)); btnClear.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { btnClearActionPerformed(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 2; gridBagConstraints.gridy = 3; gridBagConstraints.insets = new java.awt.Insets(0, 0, 0, 10); sitePanel.add(btnClear, gridBagConstraints); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridy = 1; gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL; gridBagConstraints.weightx = 0.2; gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 0); topPane.add(sitePanel, gridBagConstraints); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 1; gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL; gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST; gridBagConstraints.weightx = 1.0; gridBagConstraints.insets = new java.awt.Insets(0, 0, 10, 0); pnlSearch.add(topPane, gridBagConstraints); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 2; pnlSearch.add(downloadLocText, gridBagConstraints); lbSearchTitle.setText("Enter key words to search"); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST; gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 0); pnlSearch.add(lbSearchTitle, gridBagConstraints); jTabbedPane1.addTab("Search", pnlSearch); pnlSettings.setLayout(new java.awt.GridBagLayout()); jLabel3.setText("Download sites"); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST; gridBagConstraints.insets = new java.awt.Insets(10, 10, 5, 0); pnlSettings.add(jLabel3, gridBagConstraints); jPanel2.setLayout(new java.awt.GridBagLayout()); btnAddSite.setText("Add"); btnAddSite.setPreferredSize(new java.awt.Dimension(65, 23)); btnAddSite.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { btnAddSiteActionPerformed(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 0; gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 20); jPanel2.add(btnAddSite, gridBagConstraints); btnEditSite.setText("Edit"); btnEditSite.setPreferredSize(new java.awt.Dimension(65, 23)); btnEditSite.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { btnEditSiteActionPerformed(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 1; gridBagConstraints.gridy = 0; gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 20); jPanel2.add(btnEditSite, gridBagConstraints); btnDeleteSite.setText("Delete"); btnDeleteSite.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { btnDeleteSiteActionPerformed(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 2; gridBagConstraints.gridy = 0; gridBagConstraints.insets = new java.awt.Insets(5, 0, 0, 20); jPanel2.add(btnDeleteSite, gridBagConstraints); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 2; gridBagConstraints.insets = new java.awt.Insets(0, 0, 5, 0); pnlSettings.add(jPanel2, gridBagConstraints); lstDownloadSites.setModel(new javax.swing.AbstractListModel() { String[] strings = { "Item 1", "Item 2" }; public int getSize() { return strings.length; } public Object getElementAt(int i) { return strings[i]; } }); jScrollPane1.setViewportView(lstDownloadSites); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 1; gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH; gridBagConstraints.weightx = 1.0; gridBagConstraints.weighty = 1.0; gridBagConstraints.insets = new java.awt.Insets(0, 10, 5, 10); pnlSettings.add(jScrollPane1, gridBagConstraints); jTabbedPane1.addTab("Settings", pnlSettings); jSplitPane2.setLeftComponent(jTabbedPane1); jPanel3.setLayout(new java.awt.GridBagLayout()); availablePluginsLabel.setText("Plugins available for download from:"); availablePluginsLabel.setEnabled(false); availablePluginsLabel.setFocusable(false); availablePluginsLabel.setInheritsPopupMenu(false); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST; gridBagConstraints.insets = new java.awt.Insets(10, 10, 5, 0); jPanel3.add(availablePluginsLabel, gridBagConstraints); versionCheck.setText("Show only plugins verified to work in this release"); versionCheck.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0)); versionCheck.setMargin(new java.awt.Insets(0, 0, 0, 0)); versionCheck.addItemListener(new java.awt.event.ItemListener() { public void itemStateChanged(java.awt.event.ItemEvent evt) { versionCheckItemStateChanged(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 1; gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST; gridBagConstraints.insets = new java.awt.Insets(5, 10, 5, 0); jPanel3.add(versionCheck, gridBagConstraints); jSplitPane1.setDividerLocation(250); jSplitPane1.setPreferredSize(new java.awt.Dimension(400, 326)); treeScrollPane.setViewportView(pluginTree); jSplitPane1.setLeftComponent(treeScrollPane); infoScrollPane.setViewportView(infoTextPane); jSplitPane1.setRightComponent(infoScrollPane); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridy = 2; gridBagConstraints.gridwidth = 2; gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH; gridBagConstraints.weightx = 1.0; gridBagConstraints.weighty = 1.0; gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10); jPanel3.add(jSplitPane1, gridBagConstraints); msgLabel.setText("Messages:"); msgLabel.setEnabled(false); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 0; gridBagConstraints.gridy = 3; gridBagConstraints.anchor = java.awt.GridBagConstraints.WEST; gridBagConstraints.insets = new java.awt.Insets(10, 10, 5, 0); jPanel3.add(msgLabel, gridBagConstraints); msgPanel.setBackground(new java.awt.Color(230, 230, 230)); msgPanel.setColumns(20); msgPanel.setEditable(false); msgPanel.setLineWrap(true); msgPanel.setRows(5); msgPanel.setWrapStyleWord(true); msgPanel.setMinimumSize(new java.awt.Dimension(30, 50)); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridy = 4; gridBagConstraints.gridheight = 2; gridBagConstraints.fill = java.awt.GridBagConstraints.HORIZONTAL; gridBagConstraints.weightx = 1.0; gridBagConstraints.insets = new java.awt.Insets(0, 10, 10, 20); jPanel3.add(msgPanel, gridBagConstraints); bottomPane.setLayout(new java.awt.GridBagLayout()); buttonPanel.setLayout(new java.awt.GridBagLayout()); installDeleteButton.setText("Install"); installDeleteButton.setEnabled(false); installDeleteButton.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { installDeleteButtonActionPerformed(evt); } }); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 10); buttonPanel.add(installDeleteButton, gridBagConstraints); closeButton.setText("Close"); closeButton.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(java.awt.event.ActionEvent evt) { closeButtonActionPerformed(evt); } }); buttonPanel.add(closeButton, new java.awt.GridBagConstraints()); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridx = 1; gridBagConstraints.gridy = 1; gridBagConstraints.anchor = java.awt.GridBagConstraints.EAST; gridBagConstraints.insets = new java.awt.Insets(0, 20, 0, 20); bottomPane.add(buttonPanel, gridBagConstraints); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.gridy = 4; jPanel3.add(bottomPane, gridBagConstraints); jSplitPane2.setRightComponent(jPanel3); gridBagConstraints = new java.awt.GridBagConstraints(); gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH; gridBagConstraints.weightx = 1.0; gridBagConstraints.weighty = 1.0; getContentPane().add(jSplitPane2, gridBagConstraints); pack(); }// private void btnDeleteSiteActionPerformed(java.awt.event.ActionEvent evt) { DataSource theDataSource = (DataSource)this.lstDownloadSites.getSelectedValue(); if (theDataSource.getName().equalsIgnoreCase("Cytoscape")){ JOptionPane.showMessageDialog(this, "Your can not delete default Cytoscape site", "Warning", JOptionPane.WARNING_MESSAGE); return; } int confirm = JOptionPane.showConfirmDialog(this,"Are you sure you want to " + "delete this site","Delete Confirm",JOptionPane.OK_CANCEL_OPTION); if (confirm == JOptionPane.OK_OPTION){ BookmarksUtil.deleteBookmark(theBookmarks, bookmarkCategory, theDataSource); loadBookmarkCMBox(true); // reload is required to update the GUI } } private void btnEditSiteActionPerformed(java.awt.event.ActionEvent evt) { DataSource theDataSource = (DataSource) this.lstDownloadSites.getSelectedValue(); EditBookmarkDialog theEditDialog = new EditBookmarkDialog(this, true, theBookmarks, bookmarkCategory, "edit", theDataSource); theEditDialog.setLocationRelativeTo(this); theEditDialog.setVisible(true); loadBookmarkCMBox(true); } private void btnAddSiteActionPerformed(java.awt.event.ActionEvent evt) { EditBookmarkDialog theNewDialog = new EditBookmarkDialog(this, true, theBookmarks, bookmarkCategory, "new", null); theNewDialog.setLocationRelativeTo(this); theNewDialog.setVisible(true); theNewDialog.getDataSource(); loadBookmarkCMBox(true); // reload is required to update the GUI } private void btnClearActionPerformed(java.awt.event.ActionEvent evt) { this.switchToMainDialog(); this.tfSearch.setText(""); this.btnSearch.setEnabled(false); this.versionCheck.setEnabled(true); } private void btnBackMainActionPerformed(java.awt.event.ActionEvent evt) { // TODO add your handling code here: } // Disable btnSearch if there is no text in the Search textfield private void tfSearchKeyTyped(java.awt.event.KeyEvent evt) { if (this.tfSearch.getText().trim().equals("")){ this.btnSearch.setEnabled(false); this.switchToMainDialog(); this.btnClear.setEnabled(false); this.versionCheck.setEnabled(true); } else { this.btnSearch.setEnabled(true); this.btnClear.setEnabled(true); this.versionCheck.setEnabled(false); } } private void tfSearchActionPerformed(java.awt.event.ActionEvent evt) { // Perform the same effect as the click of btnSearch //System.out.println("Entered is pressed in search textField"); btnSearchActionPerformed(null); } private void btnSearchActionPerformed(java.awt.event.ActionEvent evt) { try { Vector filteredPluginVector = PluginIndex.getSearchResult(this.tfSearch.getText().trim(),!this.versionCheck.isSelected(), downloadLocText.getText()); if (filteredPluginVector == null){ // The index does not exist, build it now //This will create new index for the AllPluginVector PluginIndex.setAllPluginVector(this.getAllPluginVector(), !this.versionCheck.isSelected(), downloadLocText.getText()); // After the index is created, we can do searching against the index filteredPluginVector = PluginIndex.getSearchResult(this.tfSearch.getText().trim(),!this.versionCheck.isSelected(), downloadLocText.getText()); } updateTreeModel(filteredPluginVector); //this.sitePanel.setVisible(false); //this.sitePanel2.setVisible(true); } catch (Exception e){ e.printStackTrace(); JOptionPane.showMessageDialog(this, "Error in build index for PluginManager!"); } } /* * --- create the tasks and task monitors to show the user what's going on * during download/install --- */ private void createInstallTask(DownloadableInfo obj, TreeNode node) { // Create Task InstallTask task = new InstallTask(obj, node); // Configure JTask Dialog Pop-Up Box JTaskConfig jTaskConfig = new JTaskConfig(); jTaskConfig.setOwner(Cytoscape.getDesktop()); jTaskConfig.displayCloseButton(false); jTaskConfig.displayStatus(true); jTaskConfig.setAutoDispose(true); jTaskConfig.displayCancelButton(true); // Execute Task in New Thread; pop open JTask Dialog Box. TaskManager.executeTask(task, jTaskConfig); DownloadableInfo info = task.getDownloadedPlugin(); if (info != null) { updateCurrent(info); cleanTree(node); } else { // TODO somehow disable the node?? } } private void cleanTree(TreeNode node) { DownloadableInfo info = (DownloadableInfo) node.getObject(); List RemovableNodes = new java.util.ArrayList(); for (int i = 0; i < node.getParent().getChildCount(); i++) { TreeNode Child = (TreeNode) node.getParent().getChildAt(i); DownloadableInfo childInfo = (DownloadableInfo) Child.getObject(); if (childInfo.getID().equals(info.getID()) && childInfo.getName().equals(info.getName())) { RemovableNodes.add(Child); } } for (TreeNode treeNode : RemovableNodes) { treeModel.removeNodeFromParent(treeNode); } } /** Returns an ImageIcon, or null if the path was invalid. */ private javax.swing.ImageIcon createImageIcon(String path, String description) { java.net.URL imgURL = getClass().getResource(path); if (imgURL != null) { return new javax.swing.ImageIcon(imgURL, description); } else { CyLogger.getLogger().warn("Couldn't find file: " + path); return null; } } private class InstallTask implements cytoscape.task.Task { private cytoscape.task.TaskMonitor taskMonitor; private DownloadableInfo infoObj; private TreeNode node; public InstallTask(DownloadableInfo Info, TreeNode Node) throws java.lang.IllegalArgumentException { String ErrorMsg = null; if (Info == null) { ErrorMsg = "DownloadableInfo object cannot be null\n"; throw new java.lang.IllegalArgumentException(ErrorMsg); } infoObj = Info; node = Node; } public void run() { if (taskMonitor == null) { throw new IllegalStateException("Task Monitor is not set."); } taskMonitor.setStatus("Installing " + infoObj.getName() + " v" + infoObj.getObjectVersion()); taskMonitor.setPercentCompleted(-1); PluginManager Mgr = PluginManager.getPluginManager(); cytoscape.plugin.Installable ins = infoObj.getInstallable(); try { infoObj = Mgr.download(infoObj, taskMonitor); taskMonitor.setStatus(infoObj.getName() + " v" + infoObj.getObjectVersion() + " download complete."); PluginManageDialog.this.setMessage(infoObj.toString() + " download complete."); taskMonitor.setStatus(infoObj.toString() + " installing..."); Mgr.install(infoObj); Mgr.loadPlugin(infoObj); if ( Mgr.getLoadingErrors().size() > 0 ) { // since we're only loading one plugin, presumably there will only // be one throwable... Throwable t = Mgr.getLoadingErrors().get(0); Mgr.clearErrorList(); throw new PluginException("Failed to load plugin: " + infoObj.toString(),t); } taskMonitor.setStatus(infoObj.toString() + " install complete."); } catch (java.io.IOException ioe) { taskMonitor.setException(ioe, "Failed to download " + infoObj.getName() + " from " + infoObj.getObjectUrl()); logger.warn("Failed to download " + infoObj.getName() + " from " + infoObj.getObjectUrl(), ioe); infoObj = null; } catch (ManagerException me) { PluginManageDialog.this.setError("Failed to install " + infoObj.toString()); logger.warn("Failed to install " + infoObj.toString(), me); taskMonitor.setException(me, me.getMessage()); infoObj = null; } catch (PluginException pe) { PluginManageDialog.this.setError("Failed to install " + infoObj.toString()); logger.warn("Failed to install " + infoObj.toString(), pe); taskMonitor.setException(pe, pe.getMessage()); infoObj = null; } catch (ClassNotFoundException cne) { PluginManageDialog.this.setError("Failed to install " + infoObj.toString()); logger.warn("Failed to install " + infoObj.toString(), cne); taskMonitor.setException(cne, cne.getMessage()); infoObj = null; } finally { taskMonitor.setPercentCompleted(100); } try { if (infoObj == null) ins.uninstall(); } catch (ManagerException me) { logger.warn("Failed to cleanup after installation failure", me); } } public DownloadableInfo getDownloadedPlugin() { return infoObj; } public void halt() { // not haltable } public void setTaskMonitor(TaskMonitor monitor) throws IllegalThreadStateException { this.taskMonitor = monitor; } public String getTitle() { return "Installing Cytoscape " + infoObj.getType().name() + " '" + infoObj.getName() + "'"; } } // Variables declaration - do not modify private javax.swing.JLabel availablePluginsLabel; private javax.swing.JPanel bottomPane; private javax.swing.JButton btnAddSite; private javax.swing.JButton btnClear; private javax.swing.JButton btnDeleteSite; private javax.swing.JButton btnEditSite; private javax.swing.JButton btnSearch; private javax.swing.JPanel buttonPanel; private javax.swing.JButton closeButton; private javax.swing.JLabel downloadLocText; private javax.swing.JScrollPane infoScrollPane; private javax.swing.JEditorPane infoTextPane; private javax.swing.JButton installDeleteButton; private javax.swing.JLabel jLabel3; private javax.swing.JPanel jPanel2; private javax.swing.JPanel jPanel3; private javax.swing.JScrollPane jScrollPane1; private javax.swing.JSplitPane jSplitPane1; private javax.swing.JSplitPane jSplitPane2; private javax.swing.JTabbedPane jTabbedPane1; private javax.swing.JLabel lbSearchTitle; private javax.swing.JList lstDownloadSites; private javax.swing.JLabel msgLabel; private javax.swing.JTextArea msgPanel; private javax.swing.JTree pluginTree; private javax.swing.JPanel pnlSearch; private javax.swing.JPanel pnlSettings; private javax.swing.JPanel sitePanel; private javax.swing.JTextField tfSearch; private javax.swing.JPanel topPane; private javax.swing.JScrollPane treeScrollPane; private javax.swing.JCheckBox versionCheck; // End of variables declaration private TreeNode rootTreeNode; private TreeNode installedNode; private TreeNode availableNode; private ManagerModel treeModel; private TreeCellRenderer treeRenderer; private java.util.HashMap> hiddenNodes; // loads the combo box for bookmarks private void loadBookmarkCMBox(boolean selectLast) { DefaultComboBoxModel theModel = new DefaultComboBoxModel(); // Extract the URL entries List theDataSourceList = BookmarksUtil.getDataSourceList( bookmarkCategory, theBookmarks.getCategory()); if (theDataSourceList != null) { for (DataSource Current : theDataSourceList) { theModel.addElement(Current); if (selectLast) theModel.setSelectedItem(Current); } } this.lstDownloadSites.setModel(theModel); } private String bookmarkCategory = "plugins"; private Bookmarks theBookmarks; /* * Sets up the bookmarks for plugin download sites */ private void bookmarksSetUp() { try { theBookmarks = Cytoscape.getBookmarks(); } catch (Exception E) { JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "Failed to retrieve bookmarks for plugin download sites.", "Error", JOptionPane.ERROR_MESSAGE); logger.warn("Failed to retrieve bookmarks for plugin download sites.", E); return; } // if theBookmarks does not exist, create an empty one if (theBookmarks == null) { theBookmarks = new Bookmarks(); Cytoscape.setBookmarks(theBookmarks); } } private static final Color HIGHLIGHT_COLOR = new Color(0, 0, 128); // required to make the text of the data source show up correctly in the // combo box private class BookmarkCellRenderer extends JLabel implements ListCellRenderer { public BookmarkCellRenderer() { setOpaque(true); } public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) { DataSource dataSource = (DataSource) value; setText(dataSource.getName()); setToolTipText(dataSource.getHref()); if (isSelected) { setBackground(HIGHLIGHT_COLOR); setForeground(Color.white); } else { setBackground(Color.white); setForeground(Color.black); } return this; } } private class MyListSelectionListener implements ListSelectionListener { private int clickCount =0; public void valueChanged(ListSelectionEvent ev){ clickCount++; JList list = (JList) ev.getSource(); if (list.getSelectedIndices().length == 0){ // If nothing is selected, disable Edit/Delete button PluginManageDialog.this.btnEditSite.setEnabled(false); PluginManageDialog.this.btnDeleteSite.setEnabled(false); return; } if (clickCount % 2 == 0){ //This is a work-around to handle two events -- from mouse press and mouse release // Reset the click counter clickCount = 0; return; } DataSource dataSource = (DataSource) list.getSelectedValue(); if (dataSource.getName().equalsIgnoreCase("Cytoscape")){ // Cytoscape is the default site, user should never edit/delete it PluginManageDialog.this.btnEditSite.setEnabled(false); PluginManageDialog.this.btnDeleteSite.setEnabled(false); } else { PluginManageDialog.this.btnEditSite.setEnabled(true); PluginManageDialog.this.btnDeleteSite.setEnabled(true); } //If download site is changed, update the plugin tree String urlStr = dataSource.getHref(); if (!PluginManageDialog.this.currentPluginSiteURL.equalsIgnoreCase(urlStr)){ PluginManageDialog.this.currentPluginSiteURL = urlStr; PluginManageDialog.this.refreshPluginTree(); } } } public static void main(String[] args) { PluginManageDialog pd = new PluginManageDialog(); //pd.setSiteName("Testing"); List Plugins = new java.util.ArrayList(); PluginInfo infoC = new PluginInfo("1", "A Plugin"); infoC.addCytoscapeVersion(cytoscape.CytoscapeVersion.version); Plugins.add(infoC); infoC = new PluginInfo("2", "B Plugin"); infoC.addCytoscapeVersion(cytoscape.CytoscapeVersion.version); Plugins.add(infoC); infoC = new PluginInfo("3", "C"); infoC.addCytoscapeVersion(cytoscape.CytoscapeVersion.version); Plugins.add(infoC); pd.addCategory(cytoscape.plugin.Category.NONE.toString(), Plugins, PluginInstallStatus.AVAILABLE); List Outdated = new java.util.ArrayList(); PluginInfo infoOD = new PluginInfo("11", "CyGoose"); infoOD.addCytoscapeVersion("2.3"); Outdated.add(infoOD); infoOD = new PluginInfo("12", "Y"); infoOD.addCytoscapeVersion("2.3"); Outdated.add(infoOD); pd.addCategory("Outdated", Outdated, PluginInstallStatus.AVAILABLE); pd.setMessage("Foo bar"); pd.setVisible(true); } }