[BioRuby] GSoC week 2 status report

[Clayton Wheeler]

Hi all,

Here's my report on last week's work:

http://csw.github.com/bioruby-maf/blog/2012/05/21/week_2_progress/

This was my second week of work on my GSoC project, and the last week of the ‘community bonding’ period before the official start of coding. A major focus of mine was BioRuby’s phyloXML support; it uses libxml, which has been causing unit test failures under JRuby. In the end, the best course of action seemed to separate the phyloXML support as a separate plugin, which I have done as the bio-phyloxml gem. This will remove BioRuby’s dependency on XML libraries entirely and that JRuby issue along with it. At the same time, users of the phyloXML code should be able to continue using it with no substantive changes.

Separately, I began porting this phyloXML code to use Nokogiri instead of libxml-ruby, but ran into difficulties with this effort. While it is possible, and the library APIs are very similar, the code uses relatively low-level XML processing APIs in ways that seem to be sensitive to subtle differences in text node and namespace semantics between the two libraries. Substantial restructuring of the code and the addition of quite a few unit tests might be necessary to carry out such a port with confidence that the resulting code would work well.

Also, someone else submitted a JRuby patch for JRUBY-6658, one of the major causes of BioRuby’s unit test failures with JRuby; once a fix is integrated, we’ll be close to having all the tests passing under JRuby.

I identified another JRuby bug, JRUBY-6666, causing several unit test failures. This one affects BioRuby’s code for running external commands, so it would be likely to be encountered in production use. For this one, I also worked up a patch.

I also spent some time preparing a performance testing environment, for evaluating existing MAF implementations as well as my own. This will be important, since I will be considering the use of an existing C parser. I will also want to ensure that the performance of my code is competitive with the alternatives. Lacking any hardware more powerful than a MacBook Air, I am setting this up with Amazon EC2. To simplify environment setup, I’ll be using Chef. I’ve already set up a Chef repository with configuration logic, and some rudimentary code to streamline launching Ubuntu machines on EC2 and bootstrapping a Chef environment. To save money, I plan to make use of EC2 Spot Instances, which are perfect for instances that only need to run for a few hours for batch tasks.

Clayton Wheeler
cswh at umich.edu