Author: kono
Date: 2010-07-23 20:10:09 -0700 (Fri, 23 Jul 2010)
New Revision: 21020
Added:
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby.jar
Removed:
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-complete-1.4.0.jar
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-embed-0.1.3.jar
Modified:
csplugins/trunk/ucsd/kono/JRubyEngine/build.xml
csplugins/trunk/ucsd/kono/JRubyEngine/lib/ScriptEngineManager.jar
csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
Log:
RubyEngine version 0.3.
Modified: csplugins/trunk/ucsd/kono/JRubyEngine/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/build.xml 2010-07-24 03:08:13 UTC
(rev 21019)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/build.xml 2010-07-24 03:10:09 UTC
(rev 21020)
@@ -9,7 +9,7 @@
<project name="RubyScriptingEngine" default="all" basedir=".">
- <property name="jruby.version" value="jruby-1.4.0" />
+ <property name="jruby.version" value="jruby-1.5.1" />
<!-- You need modify this to your Cytoscape -->
<property name="cytoscape.dir" value="../cytoscape" />
Modified: csplugins/trunk/ucsd/kono/JRubyEngine/lib/ScriptEngineManager.jar
===================================================================
(Binary files differ)
Deleted: csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-complete-1.4.0.jar
===================================================================
(Binary files differ)
Deleted: csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-embed-0.1.3.jar
===================================================================
(Binary files differ)
Added: csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby.jar
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props 2010-07-24 03:08:13 UTC
(rev 21019)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props 2010-07-24 03:10:09 UTC
(rev 21020)
@@ -5,13 +5,13 @@
# Description used to give users information about the plugin such as what it
does.
# Html tags are encouraged for formatting purposes.
-pluginDescription=<p>Scripting Engine based on jruby 1.4.0 implementation.
The console is now integrated with BioRuby Shell.</p><p><strong><font
color="red">You need to install JRuby 1.4.0 and BioRuby 1.3.1 by
yourself.</font></strong>
+pluginDescription=<p>Scripting Engine based on jruby 1.5.1 implementation.
The console is now integrated with BioRuby Shell.</p><p><strong>You need to
install JRuby 1.5.1 and BioRuby 1.4.0 by yourself.</strong>
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=0.22
+pluginVersion=0.30
# Compatible Cytoscape version
-cytoscapeVersion=2.6, 2.7
+cytoscapeVersion=2.7, 2.8
# Category, use one of the categories listed on the website or create your own
pluginCategory=Communication/Scripting
Modified:
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
2010-07-24 03:08:13 UTC (rev 21019)
+++
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
2010-07-24 03:10:09 UTC (rev 21020)
@@ -36,15 +36,12 @@
import java.awt.event.ActionEvent;
import java.beans.PropertyChangeEvent;
-import java.io.IOException;
-import java.lang.reflect.Method;
import javax.swing.AbstractAction;
import javax.swing.Icon;
import javax.swing.ImageIcon;
import javax.swing.JMenuItem;
-import org.apache.bsf.BSFManager;
import org.jruby.embed.ScriptingContainer;
import cytoscape.Cytoscape;
@@ -60,11 +57,19 @@
*/
public class RubyEnginePlugin extends CytoscapePlugin implements
ScriptingEngine {
private static final String ENGINE_NAME = "jruby";
- private static final String ENGINE_DISPLAY_NAME = "Ruby Scripting
Engine (based on JRuby v1.4.0)";
+
+ private static final String ENGINE_VERSION = "1.5.1";
+
+ private static final String ENGINE_DISPLAY_NAME = "Ruby Scripting
Engine (JRuby v1.5.1 and BioRuby 1.4.0)";
private static final Icon ICON = new
ImageIcon(RubyEnginePlugin.class.getResource("/images/ruby.png"));
- private static final RubyEnginePlugin engine = new RubyEnginePlugin();
+ private static final Icon CONSOLE_ICON = new
ImageIcon(RubyEnginePlugin.class.getResource("/images/ruby22x22.png"));
-
+ private static RubyEnginePlugin engine = new RubyEnginePlugin();
+
+ private static final CyLogger logger = CyLogger.getLogger();
+
+ private static String jRubyHome;
+
/**
* Creates a new RubyEnginePlugin object.
*/
@@ -78,7 +83,6 @@
* @return DOCUMENT ME!
*/
public String getDisplayName() {
- // TODO Auto-generated method stub
return ENGINE_DISPLAY_NAME;
}
@@ -88,7 +92,6 @@
* @return DOCUMENT ME!
*/
public Icon getIcon() {
- // TODO Auto-generated method stub
return ICON;
}
@@ -98,45 +101,56 @@
* @return DOCUMENT ME!
*/
public String getIdentifier() {
- // TODO Auto-generated method stub
return ENGINE_NAME;
}
+
+ /**
+ * Returns version number of Scripting Engine as string
+ *
+ * @return
+ */
+ public static String getEngineVersion() {
+ return ENGINE_VERSION;
+ }
+
+
+ public static String getJRubyHome() {
+ return jRubyHome;
+ }
/**
* DOCUMENT ME!
*/
public static void register() {
-// System.setProperty("jruby.home",
"/Users/kono/Library/jruby-1.4.0");
- ScriptingContainer container = new ScriptingContainer();
- BSFManager.registerScriptingEngine("jruby",
"org.jruby.embed.bsf.JRubyEngine", new String[] {ENGINE_NAME});
+ //System.setProperty("jruby.home",
"/Users/kono/Documents/jruby-1.5.1");
+ jRubyHome = System.getenv("JRUBY_HOME");
+
+ if(jRubyHome == null)
+ throw new IllegalStateException("This system does not
have enviroment variable \"JRUBY_HOME.\" Please set it and restart
Cytoscape.");
+ System.setProperty("org.jruby.embed.class.path", jRubyHome);
+ logger.info("JRuby Home Dir = " + jRubyHome);
+
+ final ScriptingContainer container = new ScriptingContainer();
+
ScriptEngineManagerPlugin.getManager().registerEngine(ENGINE_NAME, engine);
- System.out.println("*JRuby scripting engine loaded!");
+ logger.info("JRuby scripting engine registered.");
- try {
- final Class<?> engineClass =
Class.forName("edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManager");
- Method method = engineClass.getMethod("registerEngine",
- new Class[] {
String.class, ScriptingEngine.class });
- method.invoke(null, new Object[] { ENGINE_NAME, engine
});
- } catch (Exception e) {
- e.printStackTrace();
- }
-
final JMenuItem consoleMenuItem = new JMenuItem(new
AbstractAction("Open Ruby Console") {
public void actionPerformed(ActionEvent e) {
try {
CyIRBConsole.showConsole();
- } catch (IOException e1) {
-
CyLogger.getLogger().error("Ruby Colsone Error", e1);
+ } catch (Exception e1) {
+ logger.error("Could not start
JRuby Colsone", e1);
}
}
});
- consoleMenuItem.setIcon(new
ImageIcon(RubyEnginePlugin.class.getResource("/images/ruby22x22.png")));
+ consoleMenuItem.setIcon(CONSOLE_ICON);
ScriptEngineManagerPlugin.getManager().addConsoleMenu(consoleMenuItem);
- CyLogger.getLogger().info("Ruby scripting engine registered
successfully.");
+ logger.info("JRuby colsole registered.");
}
/**
@@ -145,12 +159,17 @@
* @param e DOCUMENT ME!
*/
public void propertyChange(PropertyChangeEvent e) {
+ // If already registered, ignore.
if
(ScriptEngineManagerPlugin.getManager().getEngine(ENGINE_NAME) != null)
return;
if
(e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)) {
// Register this to ScriptEngineManager.
- register();
+ try {
+ register();
+ } catch(Exception ex) {
+ logger.error("Could not register JRuby Engine
to the Manager.", ex);
+ }
}
}
}
Modified:
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
===================================================================
---
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
2010-07-24 03:08:13 UTC (rev 21019)
+++
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
2010-07-24 03:10:09 UTC (rev 21020)
@@ -44,11 +44,13 @@
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.PrintStream;
+import java.net.URL;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
+import javax.script.ScriptException;
import javax.swing.BorderFactory;
import javax.swing.ImageIcon;
import javax.swing.JEditorPane;
@@ -62,6 +64,8 @@
import org.jruby.internal.runtime.ValueAccessor;
import cytoscape.Cytoscape;
+import cytoscape.CytoscapeInit;
+import cytoscape.logger.CyLogger;
import cytoscape.view.cytopanels.CytoPanelState;
import edu.ucsd.bioeng.idekerlab.rubyengine.RubyEnginePlugin;
@@ -71,16 +75,24 @@
* @author Keiichiro Ono
*/
public class CyIRBConsole extends JPanel {
+
+ public static final String STARTUP_SCRIPT_LOCATION =
"scripting.jruby.consolestartup";
+
+ private static final long serialVersionUID = -3402131526354557834L;
+
private static CyIRBConsole console = null;
private static Ruby runtime = null;
private static final ExecutorService consoleService = Executors
- .newCachedThreadPool();
+ .newSingleThreadExecutor();
+
private static final String BIORUBY_SCRIPT_LOCATION =
"/utilscripts/biorubyshell.rb";
private static String startScript;
private static final ImageIcon tabIcon = new ImageIcon(
RubyEnginePlugin.class.getResource("/images/ruby22x22.png"));
+ private static final CyLogger logger = CyLogger.getLogger();
+
/**
* Creates a new CyIRBConsole object.
*
@@ -88,14 +100,28 @@
* DOCUMENT ME!
* @throws IOException
*/
- public CyIRBConsole(String title) throws IOException {
- // super(title);
+ public CyIRBConsole() throws IOException {
+ final String scriptLocation = CytoscapeInit.getProperties()
+ .getProperty(STARTUP_SCRIPT_LOCATION);
+ final URL scriptURL;
+ if (scriptLocation == null) {
+ scriptURL = RubyEnginePlugin.class
+ .getResource(BIORUBY_SCRIPT_LOCATION);
+ logger.info("Default initialization script will be used
for JRuby Console.");
+ } else {
+ scriptURL = new URL(scriptLocation);
+ logger.info("Custom initialization script found for
JRuby Console: " + scriptURL.toString());
+ }
+ extractScript(scriptURL);
+ }
+
+
+ private void extractScript(final URL scriptURL) throws IOException {
InputStreamReader in = null;
StringBuilder builder = new StringBuilder();
- in = new InputStreamReader(RubyEnginePlugin.class.getResource(
- BIORUBY_SCRIPT_LOCATION).openStream());
+ in = new InputStreamReader(scriptURL.openStream());
BufferedReader br = new BufferedReader(in);
@@ -118,39 +144,72 @@
* DOCUMENT ME!
*
* @throws IOException
+ * @throws ScriptException
*/
- public static void showConsole() throws IOException {
+ public static void showConsole() throws IOException, ScriptException {
if (console == null) {
// Initialize console
- if (runtime == null)
+
+ if (runtime == null) {
runtime = Ruby.newInstance();
-
- console = new CyIRBConsole("Cytoscape-Ruby Interactive
Console");
+ final String rubyHome =
RubyEnginePlugin.getJRubyHome();
+ if (rubyHome == null)
+ throw new IllegalStateException(
+ "This system does not
have enviroment variable \"JRUBY_HOME.\" Please set it and restart
Cytoscape.");
+ else
+ runtime.setJRubyHome(rubyHome);
+ }
+ console = new CyIRBConsole();
+
buildConsole(null);
+ Cytoscape
+ .getDesktop()
+ .getCytoPanel(SwingConstants.EAST)
+ .add("BioRuby Console (Powered by JRuby
"
+ +
RubyEnginePlugin.getEngineVersion() + ")",
+ tabIcon, console);
-
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST).add(
- "Cytoscape-BioRuby Console", tabIcon,
console);
-
-
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST).setState(
- CytoPanelState.DOCK);
+ Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
+ .setState(CytoPanelState.DOCK);
}
- consoleService.execute(new Runnable() {
- public void run() {
- runtime.evalScriptlet(startScript);
+ try {
+ consoleService.execute(new Runnable() {
-
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
- .remove(console);
- if
(Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
- .getCytoPanelComponentCount()
== 0)
+ private void terminate() {
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
-
.setState(CytoPanelState.HIDE);
- runtime.tearDown();
- console = null;
- System.out.println("Console terminated!");
- }
- });
+ .remove(console);
+ if (Cytoscape.getDesktop()
+
.getCytoPanel(SwingConstants.EAST)
+
.getCytoPanelComponentCount() == 0)
+ Cytoscape.getDesktop()
+
.getCytoPanel(SwingConstants.EAST)
+
.setState(CytoPanelState.HIDE);
+ runtime.tearDown();
+ console = null;
+ logger.info("JRuby Console
terminated.");
+ }
+
+ public void run() {
+ try {
+
runtime.evalScriptlet(startScript);
+ } catch (Exception ex) {
+ ex.printStackTrace();
+ logger.error("Could not
initialize BioRuby Console.",
+ new
ScriptException(ex));
+ terminate();
+ return;
+ }
+
+ terminate();
+ }
+ });
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw new ScriptException(e);
+ }
+
}
/**
@@ -161,16 +220,17 @@
*/
public static void buildConsole(final String[] args) {
console.setLayout(new BorderLayout());
- console.setPreferredSize(new Dimension(500, 600));
+ console.setPreferredSize(new Dimension(600, 600));
final JEditorPane text = new JTextPane();
+ text.setPreferredSize(new Dimension(600, 600));
text.setMargin(new Insets(8, 8, 8, 8));
text.setCaretColor(new Color(0xa4, 0x00, 0x00));
text.setBackground(Color.white);
text.setForeground(Color.red);
- final Font font = console.findFont("Monospaced", Font.PLAIN, 14,
- new String[] { "Monaco", "Andale Mono" });
+ final Font font = console.findFont("SansSerif", Font.PLAIN, 14,
+ new String[] { "Menlo", "Monaco", "Andale Mono"
});
text.setFont(font);
final JScrollPane pane = new JScrollPane();
@@ -190,8 +250,6 @@
setOutput(new
PrintStream(tar.getOutputStream()));
setError(new
PrintStream(tar.getOutputStream()));
setObjectSpaceEnabled(true); // useful for code
completion
- // inside the IRB
- // setArgv(args);
}
};
@@ -209,8 +267,11 @@
private Font findFont(String otherwise, int style, int size,
String[] families) {
- String[] fonts =
GraphicsEnvironment.getLocalGraphicsEnvironment()
- .getAvailableFontFamilyNames();
+
+ // Get all available fonts
+ final String[] fonts = GraphicsEnvironment
+
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
+
Arrays.sort(fonts);
Font font = null;
Modified: csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
2010-07-24 03:08:13 UTC (rev 21019)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
2010-07-24 03:10:09 UTC (rev 21020)
@@ -1,9 +1,7 @@
$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/1.8'
-$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/gems/1.8/gems/bio-1.3.1/lib'
-$LOAD_PATH << ENV['HOME'] + '/.gem/ruby/1.8/gems/bio-1.3.1/lib'
+$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/site_ruby/shared'
+$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/gems/1.8/gems/bio-1.4.0/lib'
-#puts "LOAD_PATH: " + $:.inspect
-
require 'bio'
require 'bio/shell'
@@ -15,7 +13,6 @@
Bio::Shell::Setup.new
Bio::Shell.load_session
-
if Bio::Shell.cache[:rails]
Bio::Shell.cache[:rails].join
else
--
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