Author: kono
Date: 2009-12-04 15:10:29 -0800 (Fri, 04 Dec 2009)
New Revision: 18668
Added:
csplugins/trunk/ucsd/kono/ScriptEngineManager/build.xml
csplugins/trunk/ucsd/kono/ScriptEngineManager/images/
csplugins/trunk/ucsd/kono/ScriptEngineManager/images/gnome-terminal.png
csplugins/trunk/ucsd/kono/ScriptEngineManager/images/stock_run-macro.png
csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/
csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/bsf.jar
csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/commons-logging-1.1.jar
csplugins/trunk/ucsd/kono/ScriptEngineManager/plugin.props
csplugins/trunk/ucsd/kono/ScriptEngineManager/resources/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManager.java
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManagerPlugin.java
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/engine/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/engine/ScriptingEngine.java
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ui/
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ui/SelectScriptDialog.java
Log:
New Script Engine manager.
Added: csplugins/trunk/ucsd/kono/ScriptEngineManager/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/ScriptEngineManager/build.xml
(rev 0)
+++ csplugins/trunk/ucsd/kono/ScriptEngineManager/build.xml 2009-12-04
23:10:29 UTC (rev 18668)
@@ -0,0 +1,89 @@
+<?xml version="1.0"?>
+<!-- Script engine manager for Cytoscape by Kei Ono -->
+
+<project name="ScriptEngineManager" default="all" basedir=".">
+
+ <!-- The build directory -->
+ <!-- All files generated by ant go here -->
+ <property name="build.dir" value="${basedir}/build" />
+
+ <!-- The java source directory-->
+ <property name="src.dir" value="${basedir}/src" />
+
+ <property name="project.jar" value="ScriptEngineManager.jar" />
+
+ <!-- ============ Compilation Control Options =======================
-->
+ <property name="compile.debug" value="true" />
+ <property name="compile.deprecation" value="true" />
+ <property name="compile.optimize" value="true" />
+ <property name="cytoscape.dir" value="../cytoscape" />
+
+ <!-- ==================== Compilation Classpath ======================
-->
+ <path id="compile.classpath">
+ <fileset dir="${cytoscape.dir}">
+ <include name="cytoscape.jar" />
+ </fileset>
+ <fileset dir="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset>
+ </path>
+
+ <!-- ==================== Clean Target ===============================
-->
+ <target name="clean" description="Deletes all build files and starts
fresh">
+ <delete dir="${build.dir}" />
+ <delete file="${project.jar}" />
+ </target>
+
+ <!-- ==================== Compile Target
==============================-->
+ <target name="compile" depends="prepare" description="Compiles all Java
source files">
+ <mkdir dir="${build.dir}/classes" />
+ <javac srcdir="${src.dir}" source="1.5"
destdir="${build.dir}/classes" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}">
+ <classpath refid="compile.classpath" />
+ </javac>
+ </target>
+
+ <!-- ==================== Jar Target ============================== -->
+ <target name="jar" depends="compile" description="Creates Plugin Jar:
${project.jar}">
+
+ <unjar dest="${build.dir}/classes">
+ <fileset dir="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset>
+
+ </unjar>
+
+ <copy todir="${build.dir}/classes/images">
+ <fileset dir="${basedir}/images" />
+ </copy>
+
+ <copy
todir="${build.dir}/classes/edu/ucsd/bioeng/idekerlab/scriptenginemanager"
file="${basedir}/plugin.props" />
+
+ <jar destfile="${project.jar}" basedir="${build.dir}/classes">
+
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManagerPlugin"
/>
+ </manifest>
+ </jar>
+ </target>
+
+ <!-- ==================== Build and test jar
============================== -->
+ <target name="all" depends="jar" />
+
+ <!-- ==================== Prepare Target ==============================
-->
+ <target name="prepare">
+ <!-- Create build directories as needed -->
+ <mkdir dir="${build.dir}" />
+ <mkdir dir="${build.dir}/classes" />
+
+ </target>
+
+ <!-- ==================== JUnit Test Target ===========================
-->
+ <target name="test" description="Runs all JUnit tests"
depends="compile">
+ <junit printsummary="yes" fork="yes" haltonfailure="yes">
+ <formatter type="plain" usefile="false" />
+ <test name="cytoscape.test.AllTest" />
+ <classpath refid="compile.classpath" />
+ </junit>
+ </target>
+
+</project>
Added: csplugins/trunk/ucsd/kono/ScriptEngineManager/images/gnome-terminal.png
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/ScriptEngineManager/images/gnome-terminal.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/ScriptEngineManager/images/stock_run-macro.png
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/ScriptEngineManager/images/stock_run-macro.png
___________________________________________________________________
Name: svn:executable
+ *
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/bsf.jar
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/bsf.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/commons-logging-1.1.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/ScriptEngineManager/lib/commons-logging-1.1.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/ScriptEngineManager/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/ScriptEngineManager/plugin.props
(rev 0)
+++ csplugins/trunk/ucsd/kono/ScriptEngineManager/plugin.props 2009-12-04
23:10:29 UTC (rev 18668)
@@ -0,0 +1,22 @@
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=ScriptEngineManager
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=<p>Manages scripting engines following Cytoscape scripting
engine guideline. Supporting Ruby, JavaScript, Groovy and Python.
</p><p><strong><font color="red">This plugin is for technology evaluation
purpose ONLY! Still experimental and design will be changed in the future
versions.</font></strong>
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=0.05
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6, 2.7
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Communication/Scripting
+
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD Department of Medicine
Added:
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManager.java
===================================================================
---
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManager.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManager.java
2009-12-04 23:10:29 UTC (rev 18668)
@@ -0,0 +1,182 @@
+/*
+ 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 edu.ucsd.bioeng.idekerlab.scriptenginemanager;
+
+import cytoscape.Cytoscape;
+
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.engine.ScriptingEngine;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.ui.SelectScriptDialog;
+
+import org.apache.bsf.BSFException;
+import org.apache.bsf.BSFManager;
+import org.apache.bsf.util.IOUtils;
+
+import java.awt.event.ActionEvent;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import java.io.FileReader;
+import java.io.IOException;
+
+import java.lang.reflect.Method;
+
+import java.util.Map;
+import java.util.concurrent.ConcurrentHashMap;
+
+import javax.swing.AbstractAction;
+import javax.swing.ImageIcon;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+
+
+/**
+ *
+ */
+public class ScriptEngineManager implements PropertyChangeListener {
+ private static final BSFManager manager;
+ private static final Map<String, ScriptingEngine> registeredNames = new
ConcurrentHashMap<String, ScriptingEngine>();
+ private static JMenu menu;
+ private static JMenu consoleMenu;
+
+ static {
+ manager = new BSFManager();
+ }
+
+ /**
+ * Creates a new ScriptEngineManager object.
+ */
+ public ScriptEngineManager() {
+ menu = new JMenu("Execute Scripts...");
+ menu.setIcon(new
ImageIcon(ScriptEngineManager.class.getResource("/images/stock_run-macro.png")));
+
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("Plugins").add(menu);
+
+ consoleMenu = new JMenu("Scripting Language Consoles");
+ consoleMenu.setIcon(new
ImageIcon(ScriptEngineManager.class.getResource("/images/gnome-terminal.png")));
+
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("Plugins").add(consoleMenu);
+ }
+
+ protected static BSFManager getManager() {
+ return manager;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ * @param engine DOCUMENT ME!
+ */
+ public static void registerEngine(final String id, final
ScriptingEngine engine) {
+ registeredNames.put(id, engine);
+
+ menu.add(new JMenuItem(new
AbstractAction(engine.getDisplayName()) {
+ public void actionPerformed(ActionEvent e) {
+ SelectScriptDialog.showDialog(id);
+ }
+ }));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param consoleMenuItem DOCUMENT ME!
+ */
+ public static void addConsoleMenu(final JMenuItem consoleMenuItem) {
+ consoleMenu.add(consoleMenuItem);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param engineID DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ScriptingEngine getEngine(String engineID) {
+ return registeredNames.get(engineID);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param engineName DOCUMENT ME!
+ * @param scriptFileName DOCUMENT ME!
+ * @param arguments DOCUMENT ME!
+ *
+ * @throws BSFException DOCUMENT ME!
+ * @throws IOException DOCUMENT ME!
+ */
+ public static void execute(final String engineName, final String
scriptFileName,
+ final Map<String, String> arguments)
+ throws BSFException, IOException {
+ if (BSFManager.isLanguageRegistered(engineName) == false) {
+ // Register Engine
+ System.out.println("Error: Can't find " + engineName);
+
+ return;
+ }
+
+ manager.terminate();
+
+ // This is a hack... I need to decide which version of
Scripting System is apropreate for Cytoscape 3.
+ if (engineName != "jython") {
+ final Object returnVal = manager.eval(engineName,
scriptFileName, 1, 1,
+
IOUtils.getStringFromReader(new FileReader(scriptFileName)));
+
+ if (returnVal != null) {
+ System.out.println("Return Val = [" + returnVal
+ "]");
+ }
+ } else {
+ // Jython uses special console to execute script.
+ try {
+ final Class engineClass =
Class.forName("edu.ucsd.bioeng.idekerlab.pythonengine.PythonEnginePlugin");
+ Method method =
engineClass.getMethod("executePythonScript",
+ new
Class[] { String.class });
+ Object ret = method.invoke(null, new Object[] {
scriptFileName });
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent arg0) {
+ // TODO Auto-generated method stub
+ }
+}
Added:
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManagerPlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManagerPlugin.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ScriptEngineManagerPlugin.java
2009-12-04 23:10:29 UTC (rev 18668)
@@ -0,0 +1,60 @@
+/*
+ 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 edu.ucsd.bioeng.idekerlab.scriptenginemanager;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+
+/**
+ *
+ */
+public class ScriptEngineManagerPlugin extends CytoscapePlugin {
+ private static final ScriptEngineManager manager = new
ScriptEngineManager();
+
+ /**
+ * Creates a new ScriptEngineManagerPlugin object.
+ */
+ public ScriptEngineManagerPlugin() {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static ScriptEngineManager getManager() {
+ return manager;
+ }
+}
Added:
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/engine/ScriptingEngine.java
===================================================================
---
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/engine/ScriptingEngine.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/engine/ScriptingEngine.java
2009-12-04 23:10:29 UTC (rev 18668)
@@ -0,0 +1,13 @@
+package edu.ucsd.bioeng.idekerlab.scriptenginemanager.engine;
+
+import javax.swing.Icon;
+
+public interface ScriptingEngine {
+
+ public String getIdentifier();
+
+ public String getDisplayName();
+
+ public Icon getIcon();
+
+}
Added:
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ui/SelectScriptDialog.java
===================================================================
---
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ui/SelectScriptDialog.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/ScriptEngineManager/src/edu/ucsd/bioeng/idekerlab/scriptenginemanager/ui/SelectScriptDialog.java
2009-12-04 23:10:29 UTC (rev 18668)
@@ -0,0 +1,290 @@
+/*
+ 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 edu.ucsd.bioeng.idekerlab.scriptenginemanager.ui;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+
+import cytoscape.task.ui.JTaskConfig;
+
+import cytoscape.task.util.TaskManager;
+
+import cytoscape.util.FileUtil;
+
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManager;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManagerPlugin;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.engine.ScriptingEngine;
+
+import java.awt.Color;
+
+import java.io.File;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.JDialog;
+
+
+/**
+ *
+ */
+public class SelectScriptDialog extends JDialog {
+ private static SelectScriptDialog dialog = new SelectScriptDialog(null,
true);
+ private static String currentEngineID;
+ private String scriptName = null;
+ private Map<String, String> arguments = new HashMap<String, String>();
+
+ // Variables declaration - do not modify
+ private javax.swing.JButton cancelButton;
+ private javax.swing.JButton runButton;
+ private javax.swing.JLabel titleLabel;
+ private javax.swing.JButton fileButton;
+ private javax.swing.JPanel filePanel;
+ private javax.swing.JTextField fileTextField;
+
+ // End of variables declaration
+ /**
+ * DOCUMENT ME!
+ */
+ public static void showDialog(String engineID) {
+ final ScriptingEngine engine =
ScriptEngineManagerPlugin.getManager().getEngine(engineID);
+
+ if (engine == null)
+ return;
+
+ currentEngineID = engineID;
+ dialog.titleLabel.setIcon(engine.getIcon());
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.pack();
+ dialog.setVisible(true);
+ }
+
+ /**
+ * Creates a new SelectScriptDialog object.
+ *
+ * @param parent DOCUMENT ME!
+ * @param modal DOCUMENT ME!
+ */
+ public SelectScriptDialog(java.awt.Frame parent, boolean modal) {
+ super(parent, modal);
+ initComponents();
+ pack();
+ repaint();
+ }
+
+ private void initComponents() {
+ // Background color for this plugin panel.
+ this.getContentPane().setBackground(Color.white);
+ titleLabel = new javax.swing.JLabel();
+ titleLabel.setBackground(Color.white);
+ filePanel = new javax.swing.JPanel();
+ filePanel.setBackground(Color.white);
+ fileTextField = new javax.swing.JTextField();
+ fileTextField.setBackground(Color.white);
+ fileButton = new javax.swing.JButton();
+ fileButton.setBackground(Color.white);
+ cancelButton = new javax.swing.JButton();
+ cancelButton.setBackground(Color.white);
+ runButton = new javax.swing.JButton();
+ runButton.setBackground(Color.white);
+
+
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+ setTitle("Execute Script");
+ setResizable(false);
+
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 16));
+ titleLabel.setText("Run Script from File");
+
+
filePanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Script
File",
+
javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION,
+
javax.swing.border.TitledBorder.DEFAULT_POSITION,
+
new java.awt.Font("SansSerif",
+
0, 12)));
+
+ fileButton.setText("Select");
+ fileButton.addActionListener(new
java.awt.event.ActionListener() {
+ public void
actionPerformed(java.awt.event.ActionEvent evt) {
+ fileButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout filePanelLayout = new
org.jdesktop.layout.GroupLayout(filePanel);
+ filePanel.setLayout(filePanelLayout);
+
filePanelLayout.setHorizontalGroup(filePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(org.jdesktop.layout.GroupLayout.TRAILING,
+
filePanelLayout.createSequentialGroup()
+
.addContainerGap()
+
.add(fileTextField,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
438,
+
Short.MAX_VALUE)
+
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+
.add(fileButton)
+
.addContainerGap()));
+
filePanelLayout.setVerticalGroup(filePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(filePanelLayout.createSequentialGroup()
+
.add(filePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+
.add(fileButton)
+
.add(fileTextField,
+
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)));
+
+ cancelButton.setText("Cancel");
+ cancelButton.addActionListener(new
java.awt.event.ActionListener() {
+ public void
actionPerformed(java.awt.event.ActionEvent evt) {
+ cancelButtonActionPerformed(evt);
+ }
+ });
+
+ runButton.setText("Execute");
+ runButton.addActionListener(new java.awt.event.ActionListener()
{
+ public void
actionPerformed(java.awt.event.ActionEvent evt) {
+ runButtonActionPerformed(evt);
+ }
+ });
+
+ org.jdesktop.layout.GroupLayout layout = new
org.jdesktop.layout.GroupLayout(getContentPane());
+ getContentPane().setLayout(layout);
+
layout.setHorizontalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(layout.createSequentialGroup().addContainerGap()
+
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(filePanel,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
Short.MAX_VALUE).add(titleLabel)
+
.add(org.jdesktop.layout.GroupLayout.TRAILING,
+
layout.createSequentialGroup()
+
.add(runButton)
+
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+
.add(cancelButton)))
+ .addContainerGap()));
+
layout.setVerticalGroup(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(layout.createSequentialGroup().addContainerGap()
+ .add(titleLabel)
+
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+ .add(filePanel,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
org.jdesktop.layout.GroupLayout.PREFERRED_SIZE)
+
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED,
+
org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
Short.MAX_VALUE)
+
.add(layout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+
.add(cancelButton).add(runButton))
+ .addContainerGap()));
+
+ pack();
+ } // </editor-fold>
+
+ private void cancelButtonActionPerformed(java.awt.event.ActionEvent
evt) {
+ this.dispose();
+ }
+
+ private void runButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ scriptName = fileTextField.getText();
+
+ setVisible(false);
+ runScript();
+ dispose();
+ }
+
+ private void fileButtonActionPerformed(java.awt.event.ActionEvent evt) {
+ final File file = FileUtil.getFile("Select Script File",
FileUtil.LOAD);
+
+ if (file == null)
+ return;
+
+ fileTextField.setText(file.getAbsolutePath());
+ fileTextField.setToolTipText("Target Script File: " +
file.getAbsolutePath());
+ runButton.setEnabled(true);
+ }
+
+ private void runScript() {
+ // Create Task
+ Task task = new URLdownloadTask();
+
+ // Configure JTask Dialog Pop-Up Box
+ JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+ jTaskConfig.displayCancelButton(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+ }
+
+ private class URLdownloadTask implements Task {
+ private TaskMonitor taskMonitor;
+
+ public URLdownloadTask() {
+ }
+
+ public void run() {
+ taskMonitor.setStatus("Running Script: \n\n" +
scriptName + "\n\n");
+ taskMonitor.setPercentCompleted(-1);
+
+ if (scriptName != null) {
+ try {
+
ScriptEngineManager.execute(currentEngineID, scriptName, arguments);
+ } catch (Exception e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ taskMonitor.setException(e1, "Could not
finish script.");
+ }
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Finished!");
+ }
+
+ public void halt() {
+ }
+
+ public void setTaskMonitor(TaskMonitor monitor) throws
IllegalThreadStateException {
+ this.taskMonitor = monitor;
+ }
+
+ public String getTitle() {
+ return "Running Script: " + scriptName;
+ }
+ }
+}
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