Calling method from string in Ruby

A week and a little bit has passed since the beginning of coding for Google Summer of Code 2009. I am getting more and more excited since I am learning more of advanced Ruby programming.

So I am parsing XML into objects using LibXML::XML::Reader. I had this code:

 1     def parse_events()
 2       events = Events.new
 3       @reader.read #go to next element
 4       #read while have reached end of events
 5       while not(is_end_element?('events')) do
 6         if is_element?('type')
 7           @reader.read
 8           events.type = @reader.value
 9           @reader.read
10           has_reached_end_tag?('type')
11         end
12         if is_element?('duplications')
13           @reader.read
14           events.duplications = @reader.value.to_i
15           @reader.read
16           has_reached_end_tag?('duplications')
17         end
18         if is_element?('speciations')
19           @reader.read
20           events.speciations = @reader.value.to_i
21           @reader.read
22           has_reached_end_tag?('speciations')
23         end
24         if is_element?('losses')
25           @reader.read
26           events.losses = @reader.value.to_i
27           @reader.read
28           has_reached_end_tag?('losses')
29         end
30         if is_element?('confidence')
31           events.confidence = parse_confidence
32         end
33         @reader.read
34       end
35       return events
36     end #parse_events

This was too much of code duplication, but the problem was that each time different method of the events object is called.

After some searching on interwebs, luckily, I found out that ruby has a method send, which invokes the method identified by symbol and passes any arguments.

So I created such method:

  def parse_simple_element(object, name)
    if is_element?(name)
      @reader.read
      object.send("#{name}=", @reader.value)
      @reader.read
      has_reached_end_tag?(name)
    end
  end

So now the method parse_events() can be rewritten like this:

   def parse_events()
     events = Events.new
     @reader.read #go to next element
     while not(is_end_element?('events')) do
       ['type', 'duplications', 'speciations', 'losses'].each { |elmt|
         parse_simple_element(events, elmt)
       }
       if is_element?('confidence')
         events.confidence = parse_confidence
       end
       @reader.read
     end
     return events
   end #parse_events

Much shorter!! Now I run the unit tests and it works! No worries that I broke something while refactoring code. In cases like this I really appreciate the power of unit testing.

Hello World!

I wanted to have a blog for quite a long time, and now I have a good reason to start it: Google Summer of Code 2009.

My project is to implement phyloXML support in BioRuby and I am working for NESCent organization.

Here is the project abstract:

Phylogenetic trees are used in important applications, including phylogenomics, phylogeography, gene function prediction, cladistics and the study of molecular evolution. In order to foster successful analysis, exchange, storage and reuse of phylogenetic trees and associated data, the phyloXML format was developed. It can store all necessary information about the phylogenetic tree, like clade, sequence, name and distance. The goal of this project is to implement support for phyloXML in BioRuby.

My project page is: https://www.nescent.org/wg_phyloinformatics/PhyloSoC:PhyloXML_support_in_BioRuby

The source code is on GitHub: http://github.com/rozziite/bioruby/tree/master

I have been using Open Source software for quite a long time already and I am now excited to contribute back to community.