Installing the Ruby mysql gem

I've had issues installing the ruby mysql gem a couple of times, so I thought I'd document what finally worked here. I had Rails 2.3.8 running on the pre-installed Ruby 1.8.7 that comes with OS X 10.6. I needed to install Rails 3.x for another project. Having multiple versions of Rails is supposed to work OK, so I just did:

sudo gem install rails

Problems began here, but I flailed rather than keeping careful notes. At some point, I ended up thinking an fresh install of MySQL might help, so I installed version 5.5.9 from the DMG on dev.mysql.com. Maybe, I shoulda used MacPorts, cause that made things worse. After that, neither version of rails could connect to MySQL and my cubical-neighbors had new respect for my colorful vocabulary. Rails would fail, croaking up this cryptic message:

uninitialized constant MysqlCompat::MysqlRes

This thread helped. You need to be careful that MySQL, Ruby and MySQL/Ruby are compiled to a common architecture. You can do this by specifying ARCHFLAGS in the environment.

sudo env ARCHFLAGS="-arch x86_64" gem install --no-rdoc --no-ri mysql -- --with-mysql-config=/usr/local/mysql/bin/mysql_config

Compiling the gem properly is one step. The gem depends at run time on the mysql client library, which it needs to be able to find. Specify that, like so:

export DYLD_LIBRARY_PATH="/usr/local/mysql/lib:$DYLD_LIBRARY_PATH"

With the combination of these two clues, both versions of Rails seem to work happily.

Diagnosing problems with Ruby and Gems

A couple key commands for debugging RubyGems are gem list and gem env. Also, gem uninstall for removing the wreckage of failed attempts. Some recommend RVM, which I may try out some time. Also, I use the deprecated practice of installing gems with sudo. I guess I should learn to install them in my user directory.

The Ruby that comes with OS X 10.6, at least on my machine, looks like this:

$ /usr/bin/ruby --version
ruby 1.8.7 (2009-06-12 patchlevel 174) [universal-darwin10.0]

$ file /usr/bin/ruby
/usr/bin/ruby: Mach-O universal binary with 3 architectures
/usr/bin/ruby (for architecture x86_64): Mach-O 64-bit executable x86_64
/usr/bin/ruby (for architecture i386): Mach-O executable i386
/usr/bin/ruby (for architecture ppc7400): Mach-O executable ppc

Installing a fresh Ruby from MacPorts probably wasn't necessary, but that didn't stop me:

$ which ruby
/opt/local/bin/ruby

$ /opt/local/bin/ruby --version
ruby 1.8.7 (2011-02-18 patchlevel 334) [i686-darwin10]

$ file /opt/local/bin/ruby 
/opt/local/bin/ruby: Mach-O 64-bit executable x86_64

I hope this helps someone. This is a pain, but the same thing in Python is worse.

• Ruby on Rails With Apache/MySQL on Mac OS X

Bug in GlazedLists' AutoCompleteSupport?

I found what looks to me like a couple bugs in the AutoCompleteSupport of GlazedLists. I'm not going to talk about how cool GlazedLists is - it's very cool. I just want to document the bugs. Either that, or document that I'm a bonehead and I'm doing something bass-ackwards with a perfectly good library.

Note: I am doing something boneheaded. I'm documenting a known bug (bug 458). I spammed GlazedLists' mailing list. The first issue, selecting items from the popup, I reported as bug 469.

Here's my repro. I'm working on OS X with Java 10.5.0_16, which I suspect is a factor.

package org.cbare.testglazedlists;

import javax.swing.*;

import ca.odell.glazedlists.BasicEventList;
import ca.odell.glazedlists.EventList;
import ca.odell.glazedlists.swing.AutoCompleteSupport;


public class SpeciesChooser {
 JFrame frame;
 AutoCompleteSupport autocomplete;
 private JComboBox chooser;

 public SpeciesChooser() {
  initGui();
 }

 private void initGui() {
  Box vbox, hbox;
  frame = new JFrame("Species Chooser");
  
  vbox = Box.createVerticalBox();
  vbox.setBorder(BorderFactory.createEmptyBorder(12, 12, 12, 12));
  hbox = Box.createHorizontalBox();
  
  hbox.add(new JLabel("Select Species:"));
  chooser = new JComboBox();
  chooser.setPrototypeDisplayValue("Marmoset");
  hbox.add(chooser);
  SwingUtilities.invokeLater(new Runnable() {
   public void run() {
    autocomplete = AutoCompleteSupport.install(chooser, getSpecies());
   }
  });

  vbox.add(hbox);
  frame.add(vbox);
  frame.pack();
  frame.setVisible(true);
 }

 private EventList getSpecies() {
  EventList result = new BasicEventList();
  result.add("Marmoset");
  result.add("Monkey");
  result.add("Moose");
  result.add("Mouse");
  result.add("Spaaa");
  result.add("Spider");
  result.add("Spidooo");
  return result;
 }

 public static void main(String[] args) {
  SpeciesChooser s = new SpeciesChooser();
 }
}

I used Jing to make a little screencast of my flailing about. Instructions for the repro follow:

First, if I type a prefix which matches several item in the list, and I use the down-arrow to scroll through the matches and pick one, it fails to update the context of the text box. In my example, I type "mo" which matches, Monkey, Moose, Mouse. I press down-arrow twice to select Moose then press Enter. "Monkey" is still in the text box. If I repeat that a couple of times, the popup then shows all choices, not just those matching my prefix. Maybe that's intentional.

Second, if I type something that matches nothing in the list, say "moz" and then backspace over the "z" I get an exception. The stack trace is shown here:

Exception in thread "AWT-EventQueue-0" java.lang.IndexOutOfBoundsException: Index: 1, Size: 0
    at java.util.ArrayList.RangeCheck(ArrayList.java:546)
    at java.util.ArrayList.get(ArrayList.java:321)
    at ca.odell.glazedlists.impl.gui.ThreadProxyEventList.applyChangeToCache(ThreadProxyEventList.java:175)
    at ca.odell.glazedlists.impl.gui.ThreadProxyEventList.access$600(ThreadProxyEventList.java:68)
    at ca.odell.glazedlists.impl.gui.ThreadProxyEventList$UpdateRunner.listChanged(ThreadProxyEventList.java:237)
    at ca.odell.glazedlists.event.ListEventAssembler$ListEventFormat.fire(ListEventAssembler.java:412)
    at ca.odell.glazedlists.event.ListEventAssembler$ListEventFormat.fire(ListEventAssembler.java:409)
    at ca.odell.glazedlists.event.SequenceDependenciesEventPublisher$SubjectAndListener.firePendingEvent(SequenceDependenciesEventPublisher.java:445)
    at ca.odell.glazedlists.event.SequenceDependenciesEventPublisher.fireEvent(SequenceDependenciesEventPublisher.java:344)
    at ca.odell.glazedlists.event.ListEventAssembler.commitEvent(ListEventAssembler.java:316)
    at ca.odell.glazedlists.impl.gui.ThreadProxyEventList$UpdateRunner.run(ThreadProxyEventList.java:225)
    at ca.odell.glazedlists.impl.swing.SwingThreadProxyEventList.schedule(SwingThreadProxyEventList.java:33)
    at ca.odell.glazedlists.impl.gui.ThreadProxyEventList.listChanged(ThreadProxyEventList.java:118)
    at ca.odell.glazedlists.event.ListEventAssembler$ListEventFormat.fire(ListEventAssembler.java:412)
    at ca.odell.glazedlists.event.ListEventAssembler$ListEventFormat.fire(ListEventAssembler.java:409)
    at ca.odell.glazedlists.event.SequenceDependenciesEventPublisher$SubjectAndListener.firePendingEvent(SequenceDependenciesEventPublisher.java:445)
    at ca.odell.glazedlists.event.SequenceDependenciesEventPublisher.fireEvent(SequenceDependenciesEventPublisher.java:344)
    at ca.odell.glazedlists.event.ListEventAssembler.commitEvent(ListEventAssembler.java:316)
    at ca.odell.glazedlists.FilterList.constrained(FilterList.java:389)
    at ca.odell.glazedlists.FilterList.changeMatcher(FilterList.java:286)
    at ca.odell.glazedlists.FilterList.changeMatcherWithLocks(FilterList.java:269)
    at ca.odell.glazedlists.FilterList.access$100(FilterList.java:51)
    at ca.odell.glazedlists.FilterList$PrivateMatcherEditorListener.changedMatcher(FilterList.java:443)
    at ca.odell.glazedlists.matchers.AbstractMatcherEditor.fireChangedMatcher(AbstractMatcherEditor.java:115)
    at ca.odell.glazedlists.matchers.AbstractMatcherEditor.fireConstrained(AbstractMatcherEditor.java:73)
    at ca.odell.glazedlists.matchers.TextMatcherEditor.setTextMatcher(TextMatcherEditor.java:321)
    at ca.odell.glazedlists.matchers.TextMatcherEditor.setFilterText(TextMatcherEditor.java:292)
    at ca.odell.glazedlists.swing.AutoCompleteSupport.applyFilter(AutoCompleteSupport.java:1271)
    at ca.odell.glazedlists.swing.AutoCompleteSupport.access$2300(AutoCompleteSupport.java:209)
    at ca.odell.glazedlists.swing.AutoCompleteSupport$AutoCompleteFilter.postProcessDocumentChange(AutoCompleteSupport.java:1497)
    at ca.odell.glazedlists.swing.AutoCompleteSupport$AutoCompleteFilter.remove(AutoCompleteSupport.java:1450)
    at javax.swing.text.AbstractDocument.remove(AbstractDocument.java:572)
    at javax.swing.text.DefaultEditorKit$DeletePrevCharAction.actionPerformed(DefaultEditorKit.java:1030)
    at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1576)
    at javax.swing.JComponent.processKeyBinding(JComponent.java:2772)
    ...

In spite of my whining, GlazedLists is very well thought out and a nice piece of work. For later reference, I also reported bug 472.

Java in Firefox extension hosed again

A full-featured browser, an XUL front end, and the wealth of libraries available in Java makes for a powerful and flexible combination. The browser extension capability of Firefox, along with LiveConnect has been used by at least three extensions:

• Simile's Piggy Bank, a semantic web browser
• XQuseme, embeds a XQuery engine into the browser
• Firegoose, exchanges data between bioinformatics web sites

Most of what I've figured out about using Java from an extension came from Simile's David Huynh. Sadly, development of Piggy Bank has now "quiesced".

I don't know about the others, but Firegoose is hosed by the latest Java 6 update 10. Apparently, Java 6.10 introduces some significant changes into LiveConnect and the Java browser plugin. It's certainly good that Java in the browser is getting some attention, but I wish Java in a Firefox extension was a supported and regression tested use case (see whining here). The fact that it's such an arcane, unsupported and brittle hack is holding back what could otherwise be a nice technique.

Interest in Java in Firefox extensions appears to exist according to these posts in the MozillaZine Extension Development forum:

• getting java.security.PrivilegedActionException from JAR
• Java Based Extension Development
• Java
• Using java in an Extension, how ?
• Calling JAVA method. Chrome URL

First Problem: The error I get appears to happen when reflectively instantiating a Java array and looks like this:

Error calling method on NPObject!
[plugin exception: java.lang.IllegalArgumentException: No method
found matching name newInstance and arguments
[com.sun.java.browser.plugin2.liveconnect.v1.JavaNameSpace,
java.lang.Integer]].

Instantiating the array through reflection was, itself, a work-around for another LiveConnect issue with type conversion between Javascript arrays and Java arrays. It's barfing on line 03 below:

// from http://simile.mit.edu/repository/java-firefox-extension/firefox/chrome/content/scripts/browser-overlay.js
_toJavaUrlArray: function(a) {
 var urlArray = java.lang.reflect.Array.newInstance(java.net.URL, a.length);
 for (var i = 0; i < a.length; i++) {
  var url = a[i];
  java.lang.reflect.Array.set(
   urlArray,
   i,
   (typeof url == "string") ? new java.net.URL(url) : url
  );
 }
 return urlArray;
}

Update 1: First problem solved easily enough.

var dummyUrl = new java.net.URL("http://gaggle.systemsbiology.org");
var urlArray = java.lang.reflect.Array.newInstance(dummyUrl.getClass(), a.length);

Now, on to more hideousness:

Error calling method on NPObject!
[plugin exception: java.security.AccessControlException: access denied
(java.lang.RuntimePermission createClassLoader)].

...caused by trying to instantiate a URLClassLoader. The next-generation Java Plug-in, including in update 10, makes changes to the security policy such that calls from Javascript to Java are uniformly treated as untrusted.

Update 2: A Work-around!

A post on the java.net forum has a work-around. You can disable the "next-generation plug-in" through the Java control panel. Under the Advanced tab, open Java Plug-in, deselect Enable the next-generation Java Plug-in, then, restart Firefox. There is a bug filed whose comments seem to suggest that it will be addressed in a future release of the Java Plug-in.

Update 3: According to this thread on java.net, a fix is on the way in Java SE 6 update 12. Thanks, Sun!

More references:

• Java Firefox Extension by ancaluca
• mozilla.dev.tech.java
• java security policy reference
• Mozilla on Java in a Firefox Extension
• Simile mailing lists