[BioRuby] GSOC: Bioruby PhyloXML update 12

[Diana Jaunzeikare]

Hi Naohisa,

Thanks for the patches. I didn't realized that I had old version of
libxml-ruby on my computer. I got the newest 1.1.3 and made the code
compatible with it. I also added  the ncbi_mollusca_short.xml test file.
All changes are pushed to github.

Diana

On Mon, Sep 14, 2009 at 9:10 AM, Naohisa GOTO
<ngoto at gen-info.osaka-u.ac.jp>wrote:

> Hi Diana,
>
> On Mon, 10 Aug 2009 15:54:55 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > * Testing. added more unit tests (now writer has 9 tests, 26 assertions;
> > parser: 40 tests, 134 assertions)
>
> test/unit/bio/db/test_phyloxml_writer.rb failed with libxml-ruby 1.1.3.
> There are possibly 3 reasons.
>
> 1. Incompatible changes to XML::Document#save in libxml-ruby 0.9.6.
> The method now takes options as a hash. The following patch fixes the bug.
>
> ======================================================================
> --- a/lib/bio/db/phyloxml/phyloxml_writer.rb
> +++ b/lib/bio/db/phyloxml/phyloxml_writer.rb
> @@ -92,5 +92,5 @@ module Bio
>       #@doc.encoding = XML::Encoding::UTF_8
>
> -      @doc.save(@filename, true)
> +      @doc.save(@filename, :indent => true)
>       end
>
> @@ -126,5 +126,5 @@ module Bio
>             [:objarr, 'property', 'properties']] )
>
> -        @doc.save(@filename, @indent)
> +        @doc.save(@filename, :indent => @indent)
>       end #writer#write
>
> @@ -150,5 +150,5 @@ module Bio
>           @root << other_obj.to_xml
>         end
> -        @doc.save(@filename, @indent)
> +        @doc.save(@filename, :indent => @indent)
>       end
>
> ======================================================================
>
> 2. TypeError raised in the following tests.
>
> test_made_up_xml_file(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'
>
> test_phyloxml_examples_file(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_sequence_relation(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_tree2(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:280:in `initialize'
>
> test_phyloxml_examples_tree4(Bio::TestPhyloXMLWriter):
> TypeError: wrong argument type Float (expected String)
>    ./lib/bio/db/phyloxml/phyloxml_elements.rb:381:in `initialize'
>
> etc.
>
> The following patch fixes the error, but I'm not sure it is correct.
>
> ======================================================================
> --- a/lib/bio/db/phyloxml/phyloxml_elements.rb
> +++ b/lib/bio/db/phyloxml/phyloxml_elements.rb
> @@ -278,5 +278,5 @@ module PhyloXML
>       if branch_length != nil
>         if write_branch_length_as_subelement
> -          clade << XML::Node.new('branch_length', branch_length)
> +          clade << XML::Node.new('branch_length', branch_length.to_s)
>         else
>           clade["branch_length"] = branch_length.to_s
> @@ -379,5 +379,5 @@ module PhyloXML
>           raise "Type is a required attribute for confidence."
>         else
> -          confidence = XML::Node.new('confidence', @value.to_f)
> +          confidence = XML::Node.new('confidence', @value.to_s)
>           confidence["type"] = @type
>           return confidence
> ======================================================================
>
> 3. The file "ncbi_taxonomy_mollusca_short.xml" specified in test_init
> does not exist. Putting the file, or changing the file name can fix
> the problem.
>
>
> Thanks,
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>