From volker.roessler at googlemail.com Mon Dec 6 06:33:36 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Mon, 6 Dec 2010 12:33:36 +0100 Subject: [MOBY-dev] Possible Bug spotted Message-ID: 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: 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 From edward.kawas at gmail.com Mon Dec 6 12:41:29 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 6 Dec 2010 09:41:29 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: Message-ID: <00be01cb956c$d18b1230$74a13690$@gmail.com> 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 R?ssler 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: 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 From volker.roessler at googlemail.com Tue Dec 7 03:15:53 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Tue, 7 Dec 2010 09:15:53 +0100 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: <00be01cb956c$d18b1230$74a13690$@gmail.com> References: <00be01cb956c$d18b1230$74a13690$@gmail.com> Message-ID: 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: And if I set $data->value("false"), the xml output will be: I guess, it should rather be: The same thing seems to happen with the Integer Datatype in Moby. If it is set to 0, it will also produce -- Volker On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas 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 R?ssler > 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: > > > > 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 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From markw at illuminae.com Tue Dec 7 07:52:10 2010 From: markw at illuminae.com (Mark) Date: Tue, 07 Dec 2010 04:52:10 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> Message-ID: On Tue, 07 Dec 2010 00:15:53 -0800, Volker R?ssler wrote: > $VAR1 = bless( { > 'primitive' => '1', > 'namespace' => '', > 'value' => '1', > 'id' => '', > 'xrefs' => [] > }, 'MOSES::MOBY::Data::Boolean' ); ^^^^^^^^^^^^^^^^^^^^^^^^^^ That looks like a bug to me... shouldn't be writing the classname as a scalar... Eddie, I'm about to get on a plane - could you have a look at this? Cheers all! Mark From edward.kawas at gmail.com Wed Dec 8 11:20:28 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 8 Dec 2010 08:20:28 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> Message-ID: <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> 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 R?ssler 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: And if I set $data->value("false"), the xml output will be: I guess, it should rather be: The same thing seems to happen with the Integer Datatype in Moby. If it is set to 0, it will also produce -- Volker On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas 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 > R?ssler > 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: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 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Dec 8 11:26:43 2010 From: markw at illuminae.com (Mark) Date: Wed, 08 Dec 2010 08:26:43 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: Thanks Eddie! M On Wed, 08 Dec 2010 08:20:28 -0800, Edward Kawas 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, From volker.roessler at googlemail.com Thu Dec 9 04:15:37 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Thu, 9 Dec 2010 10:15:37 +0100 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: 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 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 R?ssler > 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: > value="true"> > > And if I set $data->value("false"), the xml output will be: > > > I guess, it should rather be: > 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:articleName="myinteger"/> > > -- > Volker > > > > On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas > 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 > > R?ssler > > 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: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 > > > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From volker.roessler at googlemail.com Thu Dec 9 04:46:17 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Thu, 9 Dec 2010 10:46:17 +0100 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: Sorry I meant "Scripts.pm", not "Makefile.PL". ;-) On Thu, Dec 9, 2010 at 10:15 AM, Volker R?ssler < 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 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 R?ssler >> 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: >> > value="true"> >> >> And if I set $data->value("false"), the xml output will be: >> >> >> I guess, it should rather be: >> > 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:articleName="myinteger"/> >> >> -- >> Volker >> >> >> >> On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas >> 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 >> > R?ssler >> > 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: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 >> > >> > >> > _______________________________________________ >> > MOBY-dev mailing list >> > MOBY-dev at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/moby-dev >> > >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From edward.kawas at gmail.com Thu Dec 9 09:29:30 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 9 Dec 2010 06:29:30 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: <003001cb97ad$7eae7550$7c0b5ff0$@gmail.com> That was strange. Anyways, I just uploaded a new version to CPAN. If you want the version you have to work, just remove the ./inc folder when you extract the contents of the module. Sorry about this, 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 R?ssler Sent: Thursday, December 09, 2010 1:46 AM To: Core developer announcements Subject: Re: [MOBY-dev] Possible Bug spotted Sorry I meant "Scripts.pm", not "Makefile.PL". ;-) On Thu, Dec 9, 2010 at 10:15 AM, Volker R?ssler < 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 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 >> R?ssler >> 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: >> > value="true"> >> >> And if I set $data->value("false"), the xml output will be: >> > moby:articleName="aa_change"/> >> >> I guess, it should rather be: >> > 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:articleName="myinteger"/> >> >> -- >> Volker >> >> >> >> On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas >> 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 >> > R?ssler >> > 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: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 >> > >> > >> > _______________________________________________ >> > MOBY-dev mailing list >> > MOBY-dev at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/moby-dev >> > >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Dec 13 16:08:17 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Dec 2010 13:08:17 -0800 Subject: [MOBY-dev] Mobycentral going offline temporarily Message-ID: <016f01cb9b09$de3c5d20$9ab51760$@gmail.com> Hi All, Just a heads up, that the server hosting the mobycentral registry will be going offline briefly (hopefully) around 10am MST time on Tuesday December 14th. Eddie From volker.roessler at googlemail.com Mon Dec 6 11:33:36 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Mon, 6 Dec 2010 12:33:36 +0100 Subject: [MOBY-dev] Possible Bug spotted Message-ID: 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: 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 From edward.kawas at gmail.com Mon Dec 6 17:41:29 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 6 Dec 2010 09:41:29 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: Message-ID: <00be01cb956c$d18b1230$74a13690$@gmail.com> 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 R?ssler 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: 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 From volker.roessler at googlemail.com Tue Dec 7 08:15:53 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Tue, 7 Dec 2010 09:15:53 +0100 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: <00be01cb956c$d18b1230$74a13690$@gmail.com> References: <00be01cb956c$d18b1230$74a13690$@gmail.com> Message-ID: 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: And if I set $data->value("false"), the xml output will be: I guess, it should rather be: The same thing seems to happen with the Integer Datatype in Moby. If it is set to 0, it will also produce -- Volker On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas 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 R?ssler > 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: > > > > 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 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From markw at illuminae.com Tue Dec 7 12:52:10 2010 From: markw at illuminae.com (Mark) Date: Tue, 07 Dec 2010 04:52:10 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> Message-ID: On Tue, 07 Dec 2010 00:15:53 -0800, Volker R?ssler wrote: > $VAR1 = bless( { > 'primitive' => '1', > 'namespace' => '', > 'value' => '1', > 'id' => '', > 'xrefs' => [] > }, 'MOSES::MOBY::Data::Boolean' ); ^^^^^^^^^^^^^^^^^^^^^^^^^^ That looks like a bug to me... shouldn't be writing the classname as a scalar... Eddie, I'm about to get on a plane - could you have a look at this? Cheers all! Mark From edward.kawas at gmail.com Wed Dec 8 16:20:28 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 8 Dec 2010 08:20:28 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> Message-ID: <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> 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 R?ssler 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: And if I set $data->value("false"), the xml output will be: I guess, it should rather be: The same thing seems to happen with the Integer Datatype in Moby. If it is set to 0, it will also produce -- Volker On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas 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 > R?ssler > 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: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 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Dec 8 16:26:43 2010 From: markw at illuminae.com (Mark) Date: Wed, 08 Dec 2010 08:26:43 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: Thanks Eddie! M On Wed, 08 Dec 2010 08:20:28 -0800, Edward Kawas 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, From volker.roessler at googlemail.com Thu Dec 9 09:15:37 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Thu, 9 Dec 2010 10:15:37 +0100 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: 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 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 R?ssler > 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: > value="true"> > > And if I set $data->value("false"), the xml output will be: > > > I guess, it should rather be: > 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:articleName="myinteger"/> > > -- > Volker > > > > On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas > 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 > > R?ssler > > 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: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 > > > > > > _______________________________________________ > > MOBY-dev mailing list > > MOBY-dev at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From volker.roessler at googlemail.com Thu Dec 9 09:46:17 2010 From: volker.roessler at googlemail.com (=?ISO-8859-1?Q?Volker_R=F6ssler?=) Date: Thu, 9 Dec 2010 10:46:17 +0100 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: Sorry I meant "Scripts.pm", not "Makefile.PL". ;-) On Thu, Dec 9, 2010 at 10:15 AM, Volker R?ssler < 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 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 R?ssler >> 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: >> > value="true"> >> >> And if I set $data->value("false"), the xml output will be: >> >> >> I guess, it should rather be: >> > 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:articleName="myinteger"/> >> >> -- >> Volker >> >> >> >> On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas >> 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 >> > R?ssler >> > 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: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 >> > >> > >> > _______________________________________________ >> > MOBY-dev mailing list >> > MOBY-dev at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/moby-dev >> > >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From edward.kawas at gmail.com Thu Dec 9 14:29:30 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 9 Dec 2010 06:29:30 -0800 Subject: [MOBY-dev] Possible Bug spotted In-Reply-To: References: <00be01cb956c$d18b1230$74a13690$@gmail.com> <007501cb96f3$d52a9c70$7f7fd550$@gmail.com> Message-ID: <003001cb97ad$7eae7550$7c0b5ff0$@gmail.com> That was strange. Anyways, I just uploaded a new version to CPAN. If you want the version you have to work, just remove the ./inc folder when you extract the contents of the module. Sorry about this, 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 R?ssler Sent: Thursday, December 09, 2010 1:46 AM To: Core developer announcements Subject: Re: [MOBY-dev] Possible Bug spotted Sorry I meant "Scripts.pm", not "Makefile.PL". ;-) On Thu, Dec 9, 2010 at 10:15 AM, Volker R?ssler < 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 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 >> R?ssler >> 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: >> > value="true"> >> >> And if I set $data->value("false"), the xml output will be: >> > moby:articleName="aa_change"/> >> >> I guess, it should rather be: >> > 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:articleName="myinteger"/> >> >> -- >> Volker >> >> >> >> On Mon, Dec 6, 2010 at 6:41 PM, Edward Kawas >> 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 >> > R?ssler >> > 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: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 >> > >> > >> > _______________________________________________ >> > MOBY-dev mailing list >> > MOBY-dev at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/moby-dev >> > >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Mon Dec 13 21:08:17 2010 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 13 Dec 2010 13:08:17 -0800 Subject: [MOBY-dev] Mobycentral going offline temporarily Message-ID: <016f01cb9b09$de3c5d20$9ab51760$@gmail.com> Hi All, Just a heads up, that the server hosting the mobycentral registry will be going offline briefly (hopefully) around 10am MST time on Tuesday December 14th. Eddie