[MOBY-dev] Possible Bug spotted

[Volker Rössler]

Sorry I meant "Scripts.pm", not "Makefile.PL". ;-)



On Thu, Dec 9, 2010 at 10:15 AM, Volker Rössler <
volker.roessler at googlemail.com> wrote:

> 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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>
>