[BioRuby] GSOC: Unit testing in BioRuby

[Michael Barton]

Hi Diana.

You could try adding a module along these lines to your test file,
inside the TestPhyloXML module.

  module TestPyloXMLData

    bioruby_root  = Pathname.new(File.join(File.dirname(__FILE__),
['..'] * 5)).cleanpath.to_s
    TEST_DATA = Pathname.new(File.join(bioruby_root, 'test', 'data',
'pyloxml')).cleanpath.to_s

    def self.example_xml
      File.join TEST_DATA, 'phyloxml_examples.xml'
    end

  end

You can then use

TestPhyloXMLData.example_xml

To return the path to the example test data file.



The code you described in your email adds the bioruby root to the
library path so you can do

require 'bio/db/phyloxml'

at the top of your test file.

Is this any help?

Cheers

Mike


2009/5/23 Diana Jaunzeikare <rozziite at gmail.com>
>
> Hi,
>
> How does unit testing in BioRuby works?
>
> I created new file /lib/bio/db/phyloxml.rb and
> test/unit/bio/db/test_phyloxml.rb  I also put some sample xml files in
> /test/unit/data/phyloxml/ directory.
>
> How can I access the data set in data directory from the test_phyloxml.rb
> file?
>
> Can I give path relative path to the data file? for example
> "../../../data/phyloxml/phyloxml_examples.xml"
>
> I saw other test files have this code:
>
> "require 'pathname'
> libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
> 'lib')).cleanpath.to_s
> $:.unshift(libpath) unless $:.include?(libpath)
> "
> Is this code for that purpose?  I am not really sure what this piece of code
> means.
>
> Thanks,
>
> Diana
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