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Debugging MediaWiki extensions with Eclipse for PHP and XDebug on Ubuntu 10.04

Tue, 2010-07-13 17:51 | by Samuel Lampa

 I ran into some troubles with the debugging with XDebug in Eclipse for PHP Developers / PDT (breakpoints stopped to take / catch, after I changed location of my www folder - which I figured out later), so I wanted to document the full setup procedure it here. I mainly followed this blog post. (Assuming you have apache and php set up!).

  • Download Eclipse for PHP developers
    • I'm using the Linux 32 bit version
    • Because of a bug with PDT for Eclipse Helios, I chose to go with Eclipse PDT SR2 for now.
  • Install XDebug by typing:
 apt-get install php5-xdebug
  • Edit /etc/php5/conf.d/xdebug.ini to look something like this:
 zend_extension=/usr/lib/php5/20090626+lfs/xdebug.so
 xdebug.remote_enable=On
 xdebug.remote_host="localhost"
 xdebug.remote_port=9000
 xdebug.remote_handler="dbgp"
 # xdebug.remote_log="/tmp/xdebug.log" 
    • The log line can be good to enable in case you run into troubles.
    • The first line can be different depending on PHP version. Use the line that you can find in the file (which is the default for your version of Ubuntu):
 /etc/php5/conf.d/xdebug.ini.ucf-dist
  • Restart apache:
 sudo apache2ctl restart

Configure Eclipse

  • Create a PHP Project. Mine is named "RDF4SMW".
  • Choose Run > Debug Configurations in Eclipse
  • Turn the configuration to your web server setup. For me, it looks like this ("smw" is the folder where MediaWiki is installed):

Custom location of www folder

Then an important thing If you have changed the location of your www folder from /var/www, then don't miss this! This was what caused the problem for me, with breakpoints not taking:

  • Click the "Configure" button in the Debug configuration screen seen above
  • Click the "Path mapping" tab
  • Configure according to the location of your www folder. My current config looks like so:
  • This should be it. Happy debugging!
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Got Eclipse for PHP up running with XDebug

Thu, 2010-05-13 04:23 | by Samuel Lampa

Got Eclipse for PHP up running now, with XDebug. Yay :) It was a snap to install on my Ubuntu box. I basically followed this and this blog post. (The Ubuntu package for XDebug is php5-xdebug).

The Eclipse dialogs had changed location and structure a little, so for my documentation, I included a screenshot of the dialog under "Run > Debug configurations" below.

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3rd Project Update (Integrating SWI-Prolog for Semantic Reasoning in Bioclipse)

Thu, 2010-04-08 14:17 | by Samuel Lampa

I just had my 3rd, and last project update presentation (before the final presenation on April 28th), presenting results from comparing the performance of the integrated SWI-Prolog against Jena and Pellet, for a spectrum similarity search query. Find the sldes below.

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A usage strategy emerges

Thu, 2009-11-12 17:31 | by Samuel Lampa

A strategy for how to work with the Bioclipse/JPL/Prolog/Blipkit combination I'm setting up, is becoming clear.

The main idea with Bioclipse, as well as with having a prolog engine available in it, is for flexible and "interactive" knitting together of knowledge. One of the main questions regarding how to use a Bioclipse/JPL/Prolog/Blipkit combination, has been where to put the bulk of knowledge integration/reasoning code? There would in principle be three options for that:

  1. Bioclipse (Javascript environment)
  2. The Blipkit-Prolog/Bioclipse integration plugin (Java code, a.k.a. "Manager methods")
  3. The prolog engine (As a prolog file)
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Testing out querying Prolog from Bioclipse

Sun, 2009-11-01 00:20 | by Samuel Lampa

My project has been more or less on hold for around a week because of exams and other stuff. Looking forward to getting some concrete things done now. While still reading up a bit on OWL, I've started taken the first steps of the prolog/blipkit integration with a simple method for querying a prolog on the form "subject, a predicate, and an object".

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"Refcards" for quickly getting into Bioclipse Plug-in development

Wed, 2009-10-14 16:00 | by Samuel Lampa

A link by Arvid led me to Dzone, where I found their "refcards": http://refcardz.dzone.com/ and after 15 minutes of reading, a lot of things, like file structure of Eclipse plug-in projects, had became much clearer.

For anyone new to Bioclipse plugin development, I think the following ones are the most relevant (especially the first two):

  • Eclipse Plug-in Development
  • Getting started with Equinox and OSGi
  • Spring Configuration
  • Spring Annotations

You will have to register at the site, and browse through the available ones in order to find them

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Eclipse boot process, classloading, incorporation of native code etc.

Wed, 2009-10-14 12:06 | by Samuel Lampa

This was a very good article on classloading and booting etc. in Bioclipse, with indispensable hints for how to best incorporate native code in eclipse plugins.

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Prolog plugin for Eclipse

Wed, 2009-10-14 10:27 | by Samuel Lampa

As a side-note, this looks interesting (Googled up by Egon), a Prolog Eclipse Plugin:

Could be interesting to combine that, in the future, with the results of my current project. Worth thinking about at least.

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[SOLVED] How to set java.library.path for an Eclipse/Bioclipse plugin?

Tue, 2009-10-13 16:38 | by Samuel Lampa

EDIT: Se solution at the bottom of the page

I'm trying to set the java.library.path system setting for my Bioclipse manager/Eclipse plugin.

Normally, if running java from command line, this variable should be set like so (According to what I've googled up):

java -Djava.library.path=/usr/local/lib/pl-5.7.15/lib/i686-linux/JavaClassName

so I have tried to add the line

-Djava.library.path="/usr/local/lib/pl-5.7.15/lib/i686-linux/"

to the arguments in "Run" > "Run configurations" for my plugin's product file, under the "arguments" tab.

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Plugin development for Bioclipse - from scratch

Thu, 2009-10-08 10:51 | by Samuel Lampa

I switched laptop recently, so I needed to set up my development environment for Bioclipse 2.2 plugin development from scratch. Since the instructions for how to do this are spread over a couple of blogs and the wiki, I used the occasion to create an integrated howto, for my own documentation as well as for anyone interested.

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