[MOBY-dev] Possible Bug spotted

[Volker Rössler]

Hi Eddie,

thanks for fixing the bug so quickly. When I was trying to install the new
version I noticed, that in the inc/module/Install the module "Makefile.PL"
seems to be missing, so the installer throws some error messages.

--
Volker

On Wed, Dec 8, 2010 at 5:20 PM, Edward Kawas <edward.kawas at gmail.com> wrote:

> Hi Volker,
>
> I tracked down this bug and fixed it. I deployed a new version of
> MOSES-MOBY
> (0.96) onto CPAN and it should be available in a couple hours.
>
> Thanks,
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker Rössler
>  Sent: Tuesday, December 07, 2010 12:16 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Possible Bug spotted
>
> Hi,
>
> thanks for your reply.
>
> When I run the script as you proposed, I get this:
>
> $VAR1 = bless( {
>                'primitive' => '1',
>                'namespace' => '',
>                'value' => '1',
>                'id' => '',
>                'xrefs' => []
>              }, 'MOSES::MOBY::Data::Boolean' );
>
> $VAR1 = bless( {
>                'primitive' => '1',
>                'namespace' => '',
>                'value' => '0',
>                'id' => '',
>                'xrefs' => []
>              }, 'MOSES::MOBY::Data::Boolean' );
>
> Which seems fine. When I dump the results in $data with the Data::Dumper in
> my webservice, I get the same results.
>
> However, If I use the same construct in my moby webservice, and pass $data
> in the "output object", the strange behaviour is showing, which I've
> described earlier.
>
>  my $output_annotated_CodingSNP = new MOSES::MOBY::Data::AnnotatedCodingSNP
>                   (
>                       wt_aa_seq => $pep_obj->get_field('wt_pep'),
>                       mut_aa_seq => $pep_obj->get_field('mutant_pep'),
>                       ext_database_refs => \@extDatabaseRefsList,
>                       codon_ref => $pep_obj->get_field('codon_reference'),
>                       aa_ref => $pep_obj->get_field('aa_reference'),
>                       codon_var => $pep_obj->get_field('codon_genotype'),
>                       aa_var => $pep_obj->get_field('aa_genotype'),
>                       aa_pos => $aa_pos,
>                       a*a_change => $data,*
>                        Position => $position,
>                       Strain => $Strain,
>                       reference_allele => $reference_allele,
>                       genotype_allele => $genetype_allele
>                   );
>
>  $response->add_output_annotated_CodingSNP($output_annotated_CodingSNP);
>
>
> If I set $data->value("true"), the xml output will be:
> <moby:Boolean moby:id="" moby:namespace="" moby:articleName="aa_change"
> value="true">
>
> And if I set $data->value("false"), the xml output will be:
> <moby:Boolean moby:id="" moby:namespace="" moby:articleName="aa_change"/>
>
> I guess, it should rather be:
>  <moby:Boolean moby:id="" moby:namespace="" moby:articleName="aa_change"
> value="false">
>
>
> The same thing seems to happen with the Integer Datatype in Moby. If it is
> set to 0, it will also produce  <moby:Integer moby:id="" moby:namespace=""
> moby:articleName="myinteger"/>
>
> --
> Volker
>
>
>
> On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas <edward.kawas at gmail.com>
> wrote:
> > What do you get when you run a script like:
> >
> > #!/usr/bin/perl -w
> >
> > use strict;
> >
> > use MOSES::MOBY::Data::Boolean;
> > use Data::Dumper;
> >
> > # create a Moby Boolean with initial value of true  my $data =
> > MOSES::MOBY::Data::Boolean->new ( value=>'true' );
> >
> >  print Dumper($data), "\n";
> >
> >  # change the value to false
> >  $data->value ('false');
> >
> >  # get the value
> >  print Dumper($data), "\n";
> >
> >
> >
> > -----Original Message-----
> > From: moby-dev-bounces at lists.open-bio.org
> > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Volker
> > Rössler
> > Sent: Monday, December 06, 2010 3:34 AM
> > To: moby-dev at lists.open-bio.org
> > Subject: [MOBY-dev] Possible Bug spotted
> >
> > Hi everyone,
> >
> > I'm trying to set a variable of type boolean in the Moby output object
> > to 'false'. The strange thing is, that I can't seem to set it to the
> > value 'false'.
> > If I try to set it to false, it will produce something like this in
> > the
> xml
> > output:
> >
> > <moby:Boolean moby:id="" moby:namespace=""
> > moby:articleName="aa_change"/>
> >
> > I have tried different approaches like this:
> > MOSES::MOBY::Data::Boolean->new(value => 'false');
> >
> > Is this a bug in Moby?
> >
> > Does anyone have a clue?
> > Thanks in advance!
> >
> > --
> > Volker
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> >
> > _______________________________________________
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> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
>
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