2009 on John Paulett

jsonpickle 0.3.1 Released

Fri, 18 Dec 2009 02:13:17 +0000

jsonpickle, the powerful library for serializing complex object graphs in Python to JSON, had a major milestone this week with the official release of 0.3.1, available on PyPi with documentation and full release notes at http://jsonpickle.github.com/. We have migrated from the Google Code site to the new Github site at http://github.com/jsonpickle/jsonpickle.

This release represents nearly a year of development from multiple contributors. Some of the major highlights of the release include supporting a wider variety of objects, supporting the pickle protocol's set and get state methods, and allowing the use and addition of any Python JSON backend (e.g. demjson, simplejson, django.util.simplejson, etc.). Please be aware that backwards compatibility for the 0.2.0 format JSON is not guaranteed.

HTML to reStructuredText in Python using Pandoc

Fri, 16 Oct 2009 00:32:18 +0000

During the conversion of my blog from Wordpress to a custom Django-based system, I wanted to move from HTML markup to reStructuredText (partly to make it easier to publish Sphinx documentation to my blog).

While it is dead simple to convert reStructuredText to HTML, going the other way is more difficult. Luckily, Pandoc, the swiss army knife for converting between markup formats, can do a nice job converting HTML to reStructuredText.

I wrote a custom Django Command to parse a Wordpress XML export file and store the blog entries. The relevant code to convert HTML to reStructuredText is very simple. It simply makes a subprocess call to the Pandoc command and retrieves the command's output. Make sure you have Pandoc installed (in Ubuntu, sudo apt-get install pandoc will work).

reStructuredText Widget in Django Admin

Thu, 15 Oct 2009 03:44:55 +0000

While Django has great support for rendering standard markup languages, sometimes it can be difficult editing documents using a markup in the Django Admin. Several others (1, 2, 3) show how easy it is to edit Markdown, Textile, and even HTML, in the Django Admin using a WYSIWYG editor, such as markItUp! or TinyMCE.

Unfortunately, reStructuredText is not well support by most WYSIWYG editors. Nevertheless, we can improve the experience of editing reStructuredText in the Django Admin. One of the biggest improvements is switching the Textarea to use a monospace font to avoid issues caused by the heading underlines being too short. We can also customize the size of the Textarea.

Mocking Groovy's HTTPBuilder

Thu, 15 Oct 2009 00:22:19 +0000

I ran into a head-scratcher today when trying to unit test some Groovy code. The code under test interacts with an HTTP web service using Groovy's great HTTPBuilder, which wraps Apache's HttpClient. Obviously, I wanted to mock the interaction with the HTTP server to limit the scope of my tests.

Groovy makes it easy to create simple mocks using maps. To mock a class with a map, one must create a map which is keyed by the methods names to be tested and storing closures for the mock method implementation. For example, if we wish to mock out the HTTPBuilder, which has a "post" method, we can accomplish it using the map defined by mapMock.

Master's Thesis & Open-Source Tool

Thu, 23 Jul 2009 03:00:49 +0000

On July 15th, I successfully defended my Master's Thesis in Biomedical Informatics at Vanderbilt University. This defense was the culmination of 2 years of work. The thesis focuses on extracting organizational structure and relationships from the audit logs of clinician information systems. This work has potential applications in the improvement of delivery of care and improving the security of patients private medical data.

As part of this work, I developed an open-source tool for analyzing audit logs. Licensed under an Apache 2.0 License, the Healthcare Organizational Relational Network Extraction Toolkit (HORNET) is a Python framework for plugins that analyze healthcare audit logs. The tool is fully functional, but is not yet polished enough for use by healthcare administrators.

Programming Clojure Review

Thu, 09 Jul 2009 16:38:32 +0000

When Stuart Halloway's Programming Clojure came out in May, I picked up a copy and have been reading through it and practicing with the Project Euler problems.

First off, it is a great book! Second off, it introduces a seriously interesting programming language.

Clojure is a Lisp dialect designed to run on Java Virtual Machine (JVM). This combination is what makes Clojure very powerful: you get the power of a mature virtual machine with access to any existing Java libraries, combined with the dynamic, functional style of Lisp. Imagine being able to continue to use the code and libraries you any others have spent years developing from a new programming environment.

Install Eclipse Galileo (3.5) on Ubuntu Jaunty (9.04)

Fri, 26 Jun 2009 16:13:40 +0000

Eclipse 3.5, codenamed "Galileo," was released this week! While there is a team actively working on building an Ubuntu deb package, they do not yet have a package yet for Eclipse 3.5. I put together some super simple instructions for installing Eclipse 3.5.

I am going to perform a per-user installation into my home-directory. If multiple people use eclipse on the same computer, you may want to modify these instructions to install into /opt/. I am going to put the installable in ~/bin/packages/eclipse3.5. First, create the installation directory (change according to your own tastes)

Vanderbilt Projects in the News

Sat, 20 Jun 2009 13:17:17 +0000

Some of the projects that I have been involved in at Vanderbilt University's Informatics Center have been featured in the news recently:

The New York Times had a feature about our use of the ILOG (now IBM) business rules engine to send out pager or SMS messages to physicians when patients have critical lab results.
Infection Control Today had an article about our Sepsis detection application which monitors patients' vital signs and lab results in real time to alert physician to patients who may have sepsis.

tdaemon and virtualenv

Tue, 16 Jun 2009 04:22:46 +0000

I ran across tdaemon, which automatically runs your test suite when you make a change to your source code. It is very helpful when developing. One issue I had was running the tests when tdaemon needs to monitor a huge number of files (as occurs when I have a virtualenv environment in the same directory, which has more than 100MB of code and binaries). I committed a few changes to tdaemon to allow the user to ignore any directories. For instance, if you want to ignore a virtualenv directory called "env" and the "build" and "dist" directories from distutils:

Move to johnpaulett.com

Sat, 13 Jun 2009 21:04:46 +0000

I have moved this blog to johnpaulett.com. Links to all old posts should still work.

Automated Testing Presentation

Fri, 17 Apr 2009 22:30:08 +0000

Getting Started with (Distributed) Version Control

Fri, 03 Apr 2009 21:50:33 +0000

I gave a short talk on using a distributed version control system. The slides are available on SlideShare under a Creative Commons license.

Parsing HL7 with Python

Sat, 10 Jan 2009 11:23:26 +0000

I've had a need to parse Health Level 7 (HL7) version 2.x messages from Python, thus I created python-hl7. The library allows for easy, key-based access of all the elements in an HL7 message. See the release announcement for download information.

HL7 is a communication protocol and message format for health care data. It is the de facto standard for transmitting data between clinical information systems and between clinical devices. The version 2.x series, which is often is a pipe delimited format is currently the most widely accepted version of HL7 (version 3.0 is an XML-based format).