[BioRuby] Bioruby unit tests

Sun Jun 14 15:22:29 UTC 2009

Thanks! This worked like a charm. Now all the tests pass.

Diana

On Sat, Jun 13, 2009 at 12:47 AM, Naohisa GOTO <ngoto at gen-info.osaka-u.ac.jp
> wrote:

> Hi Diana,
>
> This is because your original Sequence class definition in line 269
> in lib/bio/db/phyloxml.rb violates BioRuby's Bio::Sequence.
>
> The PhyloXML Sequence class (and Events, Date, Id, Uri, etc)
> should be defined inside the Bio::PhyloXML namespace.
>
> For example,
>
> module Bio
>  class PhyloXML
>    class Sequence
>      #...
>    end
>    class Events
>      #...
>    end
>    class Date
>      #...
>    end
>  end
> end
>
> In this case, Bio::PhyloXML::Sequence is different from
> Bio::Sequence.
>
> Be careful that the name Date is already used by Ruby's
> standard bundled library (require 'date'), althogh you can
> distinguish it by using ::Date and Bio::PhyloXML::Date.
>
> I also recommend that PhyloXMLTree and PhyloXMLNode are
> located inside the Bio::PhyloXML namespace (this means
> Bio::PhyloXML::PhyloXMLTree and Bio::PhyloXML::PhyloXMLNode.
> If possible, to rename to Bio::PhyloXML::Tree and
> Bio::PhyloXML::Node may be a good choice.)
>
> Naohisa Goto
> ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org
>
> On Fri, 12 Jun 2009 11:25:40 -0400
> Diana Jaunzeikare <rozziite at gmail.com> wrote:
>
> > Hi all,
> >
> > I am working on implementing phyloxml support and I was running only my
> unit
> > tests to test my code. Then yesterday I ran all of the unit tests and it
> > gave me errors (when I first cloned it did not gave me any errors). I
> don't
> > think i changed anything in any other file than lib/bio/db/phyloxml.rb
> and
> > test/unit/bio/db/test_phyloxml.rb
> >
> > Here is the output of test/runner.rb. Looks all of the errors are of the
> > same kind.
> >
> > diana at diana-ubuntu:~/bioruby$ ruby test/runner.rb
> > Loaded suite .
> > Started
> >
> .........................................................................................EE...............................................
> (snip)
> > Finished in 176.329241 seconds.
> >
> >   1) Error:
> > test_output_embl(Bio::FuncTestSequenceOutputEMBL):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:263:in `initialize'
> >     ./lib/bio/sequence.rb:263:in `new'
> >     ./lib/bio/sequence.rb:263:in `auto'
> >     ./test/functional/bio/sequence/test_output_embl.rb:21:in `setup'
> >
> >   2) Error:
> > test_output_fasta(Bio::FuncTestSequenceOutputEMBL):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:263:in `initialize'
> >     ./lib/bio/sequence.rb:263:in `new'
> >     ./lib/bio/sequence.rb:263:in `auto'
> >     ./test/functional/bio/sequence/test_output_embl.rb:21:in `setup'
> >
> >   3) Error:
> > test_alignment(Bio::TestAlignmentMultiFastaFormat):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:443:in `initialize'
> >     ./lib/bio/sequence.rb:443:in `new'
> >     ./lib/bio/sequence.rb:443:in `adapter'
> >     ./lib/bio/db/fasta.rb:221:in `to_seq'
> >     ./lib/bio/appl/mafft/report.rb:90:in `determine_seq_method'
> >     ./lib/bio/appl/mafft/report.rb:89:in `each'
> >     ./lib/bio/appl/mafft/report.rb:89:in `determine_seq_method'
> >     ./lib/bio/appl/mafft/report.rb:61:in `alignment'
> >     ./test/unit/bio/appl/mafft/test_report.rb:47:in `test_alignment'
> >
> >   4) Error:
> > test_determine_seq_method(Bio::TestAlignmentMultiFastaFormat):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:443:in `initialize'
> >     ./lib/bio/sequence.rb:443:in `new'
> >     ./lib/bio/sequence.rb:443:in `adapter'
> >     ./lib/bio/db/fasta.rb:221:in `to_seq'
> >     ./lib/bio/appl/mafft/report.rb:90:in `determine_seq_method'
> >     ./lib/bio/appl/mafft/report.rb:89:in `each'
> >     ./lib/bio/appl/mafft/report.rb:89:in `determine_seq_method'
> >     ./lib/bio/appl/mafft/report.rb:61:in `alignment'
> >     ./test/unit/bio/appl/mafft/test_report.rb:57:in
> > `test_determine_seq_method'
> >
> >   5) Error:
> > test_const_version(Bio::TestGFF3):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:443:in `initialize'
> >     ./lib/bio/sequence.rb:443:in `new'
> >     ./lib/bio/sequence.rb:443:in `adapter'
> >     ./lib/bio/db/fasta.rb:221:in `to_seq'
> >     ./lib/bio/db/gff.rb:954:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:949:in `each_line'
> >     ./lib/bio/db/gff.rb:949:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:941:in `parse'
> >     ./lib/bio/db/gff.rb:881:in `initialize'
> >     ./test/unit/bio/db/test_gff.rb:644:in `new'
> >     ./test/unit/bio/db/test_gff.rb:644:in `setup'
> >
> >   6) Error:
> > test_gff_version(Bio::TestGFF3):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:443:in `initialize'
> >     ./lib/bio/sequence.rb:443:in `new'
> >     ./lib/bio/sequence.rb:443:in `adapter'
> >     ./lib/bio/db/fasta.rb:221:in `to_seq'
> >     ./lib/bio/db/gff.rb:954:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:949:in `each_line'
> >     ./lib/bio/db/gff.rb:949:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:941:in `parse'
> >     ./lib/bio/db/gff.rb:881:in `initialize'
> >     ./test/unit/bio/db/test_gff.rb:644:in `new'
> >     ./test/unit/bio/db/test_gff.rb:644:in `setup'
> >
> >   7) Error:
> > test_records(Bio::TestGFF3):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:443:in `initialize'
> >     ./lib/bio/sequence.rb:443:in `new'
> >     ./lib/bio/sequence.rb:443:in `adapter'
> >     ./lib/bio/db/fasta.rb:221:in `to_seq'
> >     ./lib/bio/db/gff.rb:954:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:949:in `each_line'
> >     ./lib/bio/db/gff.rb:949:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:941:in `parse'
> >     ./lib/bio/db/gff.rb:881:in `initialize'
> >     ./test/unit/bio/db/test_gff.rb:644:in `new'
> >     ./test/unit/bio/db/test_gff.rb:644:in `setup'
> >
> >   8) Error:
> > test_sequence_regions(Bio::TestGFF3):
> > ArgumentError: wrong number of arguments (1 for 0)
> >     ./lib/bio/sequence.rb:443:in `initialize'
> >     ./lib/bio/sequence.rb:443:in `new'
> >     ./lib/bio/sequence.rb:443:in `adapter'
> >     ./lib/bio/db/fasta.rb:221:in `to_seq'
> >     ./lib/bio/db/gff.rb:954:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:949:in `each_line'
> >     ./lib/bio/db/gff.rb:949:in `parse_fasta'
> >     ./lib/bio/db/gff.rb:941:in `parse'
> >     ./lib/bio/db/gff.rb:881:in `initialize'
> >     ./test/unit/bio/db/test_gff.rb:644:in `new'
> >     ./test/unit/bio/db/test_gff.rb:644:in `setup'
> > [....]
> > 2175 tests, 5180 assertions, 0 failures, 54 errors
> >
> >
> > Any ideas?  Code is available here
> > http://github.com/latvianlinuxgirl/bioruby/tree/dev
> >
> > Diana
> >
>
>
>