Bug #85984 for Bio-Graphics: bug in Bio::Graphics::DrawTransmembrane constructor/defaults

Sat Jun 08 10:55:25 2013 sjpitts [...] gmail.com - Ticket created

Subject:	bug in Bio::Graphics::DrawTransmembrane constructor/defaults
Date:	Sat, 8 Jun 2013 07:55:04 -0700
To:	bug-Bio-Graphics [...] rt.cpan.org
From:	Steven Pitts <sjpitts [...] gmail.com>

While walking through the demo code in the POD documentation for Bio::Graphics::DrawTransmembrane, I discovered a bug that makes even the demo code throw an error and output an empty image file. The issue is that in the hash %DRAWOPTIONS, the default value set via the 'labels' key (which ultimately sets the default value of the Bio::Graphics::DrawTransmembrane object's 'loop_labels' property) is an array reference rather than a hash reference. All other methods dereference this as a hash ref so it renders subsequent method calls nonfunctional with 'Not a HASH reference...' errors thrown. it should be the case that $DRAWOPTIONS{'labels'}{'default'} = {}, not $DRAWOPTIONS{'labels'}{'default'} = [] as it is currently coded. Explicitly setting the loop_labels property of a Bio::Graphics::DrawTransmembrane object to a hash ref prior to calling the png method will rescue the code (try the code below with and without the ### commented portion to verify the bug). use Bio::Graphics::DrawTransmembrane; my @topology = (20,45,59,70,86,109,145,168,194,220); ## Simple use - -topology is the only option that is required my $im = Bio::Graphics::DrawTransmembrane->new( -title => 'This is a cartoon displaying transmembrane helices.', -topology => \@topology); ### without this perl throws ### Not a HASH reference at /Library/Perl/5.12/Bio/Graphics/DrawTransmembrane.pm line 125. ### $im->{loop_labels} = {}; ## Now write the image to a .png file open(OUTPUT, ">output.png"); binmode OUTPUT; print OUTPUT $im->png; close OUTPUT; Thanks for making the package available. Cheers, Steve Pitts

Sun Aug 18 02:16:01 2013 randomcoder1 [...] gmail.com - Correspondence added

Two patches to solve this problem. These patches can be applied against version 2.37 The patch to DrawTransmembrane.pm is most important and is very short. Basically loop_labels is initiatilez as a arrayref but later on it's mistaken for a hashref in some parts of the code. The second problem is in feature_draw.pl where $data->features returns an array and is mistaken for a hashref. Please consider having a look at these patches. @Steve Your code will run with these patches applied to Bio::Graphics On Sat Jun 08 10:55:25 2013, sjpitts@gmail.com wrote: Show quoted text

> While walking through the demo code in the POD documentation for > Bio::Graphics::DrawTransmembrane, I discovered a bug that makes even > the demo code throw an error and output an empty image file. > > The issue is that in the hash %DRAWOPTIONS, the default value set via > the 'labels' key (which ultimately sets the default value of the > Bio::Graphics::DrawTransmembrane object's 'loop_labels' property) is > an array reference rather than a hash reference. All other methods > dereference this as a hash ref so it renders subsequent method calls > nonfunctional with 'Not a HASH reference...' errors thrown. > > it should be the case that $DRAWOPTIONS{'labels'}{'default'} = {}, not > $DRAWOPTIONS{'labels'}{'default'} = [] as it is currently coded. > > Explicitly setting the loop_labels property of a > Bio::Graphics::DrawTransmembrane object to a hash ref prior to calling > the png method will rescue the code (try the code below with and > without the ### commented portion to verify the bug). > > use Bio::Graphics::DrawTransmembrane; > my @topology = (20,45,59,70,86,109,145,168,194,220); > > ## Simple use - -topology is the only option that is required > > my $im = Bio::Graphics::DrawTransmembrane->new( -title => 'This is a > cartoon displaying transmembrane helices.', -topology => \@topology); > > ### without this perl throws > ### Not a HASH reference at > /Library/Perl/5.12/Bio/Graphics/DrawTransmembrane.pm line 125. > ### $im->{loop_labels} = {}; > > ## Now write the image to a .png file > open(OUTPUT, ">output.png"); > binmode OUTPUT; > print OUTPUT $im->png; > close OUTPUT; > > > Thanks for making the package available. > > Cheers, > Steve Pitts >

-- Your bugs , they are afraid of me.

Subject:

DrawTransmembrane.pm.patch

From e5e186e52ddfd66408015a661ddc1f40c1bffa61 Mon Sep 17 00:00:00 2001 From: Petrea Corneliu Stefan <stefan@garage-coding.com> Date: Sun, 18 Aug 2013 08:04:44 +0200 Subject: [PATCH 1/1] added DrawTransmembrane fix --- lib/Bio/Graphics/DrawTransmembrane.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/Bio/Graphics/DrawTransmembrane.pm b/lib/Bio/Graphics/DrawTransmembrane.pm index 260b57a..838d34d 100755 --- a/lib/Bio/Graphics/DrawTransmembrane.pm +++ b/lib/Bio/Graphics/DrawTransmembrane.pm @@ -76,7 +76,7 @@ my %DRAWOPTIONS = ( 'default' => 1}, ## labeling options 'labels' => { 'private' => 'loop_labels', - 'default' => []}, + 'default' => {}}, 'text_offset' => { 'private' => 'text_offset', 'default' => 0}, 'helix_label' => { 'private' => 'helix_label', -- 1.8.1.2

Subject:

feature_draw.pl.patch

From e5e186e52ddfd66408015a661ddc1f40c1bffa61 Mon Sep 17 00:00:00 2001 From: Petrea Corneliu Stefan <stefan@garage-coding.com> Date: Sun, 18 Aug 2013 08:04:44 +0200 Subject: [PATCH 1/1] added DrawTransmembrane fix --- scripts/feature_draw.pl | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/scripts/feature_draw.pl b/scripts/feature_draw.pl index e878ad0..7357adf 100755 --- a/scripts/feature_draw.pl +++ b/scripts/feature_draw.pl @@ -31,6 +31,9 @@ my @COLORS = qw(cyan blue red yellow green wheat turquoise orange); # default c my $color = 0; # position in color cycle my $data = Bio::Graphics::FeatureFile->new(-file => '-'); +use Data::Dumper; +#print Dumper [ $data->configured_types ]; +#print Dumper [ $data->features ]; # general configuration of the image here my $width = $WIDTH || $data->setting(general => 'pixels') @@ -55,7 +58,8 @@ if (!defined $start || !defined $stop) { # over is presented in alphabetic order my %types = map {$_=>1} $data->configured_types; -my @configured_types = grep {exists $data->features->{$_}} $data->configured_types; +use List::Util qw/first/; +my @configured_types = grep { my $c_type = $_; first { $c_type eq $_ } $data->features; } $data->configured_types; my @unconfigured_types = sort grep {!exists $types{$_}} $data->types; # create the segment,the panel and the arrow with tickmarks @@ -86,7 +90,13 @@ if ($BOXES) { # debugging code debugging_rectangles($gd,$boxes); } -print $gd->can('png') ? $gd->png : $gd->gif; +if($gd->can('png')) { + print STDERR "Printing png\n"; + print $gd->png; +} elsif($gd->can('gif')) { + print STDERR "Printing gif\n"; + print $gd->gif; +}; sub debugging_rectangles { my ($image,$boxes) = @_; -- 1.8.1.2

Sun Aug 18 02:16:02 2013 The RT System itself - Status changed from 'new' to 'open'

Sun Aug 18 02:16:02 2013 randomcoder1 [...] gmail.com - Fixed in 2.37 added

Sun Aug 18 02:21:26 2013 randomcoder1 [...] gmail.com - Cc WSDOOKADR added

Sun Aug 18 18:32:43 2013 randomcoder1 [...] gmail.com - Correspondence added

Also made a pull request with the same content on github. https://github.com/GMOD/Bio-Graphics/pull/15 On Sat Jun 08 10:55:25 2013, sjpitts@gmail.com wrote: Show quoted text

> While walking through the demo code in the POD documentation for > Bio::Graphics::DrawTransmembrane, I discovered a bug that makes even > the demo code throw an error and output an empty image file. > > The issue is that in the hash %DRAWOPTIONS, the default value set via > the 'labels' key (which ultimately sets the default value of the > Bio::Graphics::DrawTransmembrane object's 'loop_labels' property) is > an array reference rather than a hash reference. All other methods > dereference this as a hash ref so it renders subsequent method calls > nonfunctional with 'Not a HASH reference...' errors thrown. > > it should be the case that $DRAWOPTIONS{'labels'}{'default'} = {}, not > $DRAWOPTIONS{'labels'}{'default'} = [] as it is currently coded. > > Explicitly setting the loop_labels property of a > Bio::Graphics::DrawTransmembrane object to a hash ref prior to calling > the png method will rescue the code (try the code below with and > without the ### commented portion to verify the bug). > > use Bio::Graphics::DrawTransmembrane; > my @topology = (20,45,59,70,86,109,145,168,194,220); > > ## Simple use - -topology is the only option that is required > > my $im = Bio::Graphics::DrawTransmembrane->new( -title => 'This is a > cartoon displaying transmembrane helices.', -topology => \@topology); > > ### without this perl throws > ### Not a HASH reference at > /Library/Perl/5.12/Bio/Graphics/DrawTransmembrane.pm line 125. > ### $im->{loop_labels} = {}; > > ## Now write the image to a .png file > open(OUTPUT, ">output.png"); > binmode OUTPUT; > print OUTPUT $im->png; > close OUTPUT; > > > Thanks for making the package available. > > Cheers, > Steve Pitts >

-- Your bugs , they are afraid of me.

Thu Aug 29 16:18:25 2013 LDS [...] cpan.org - Correspondence added

GitHub pull request accepted. Thank you!

Thu Aug 29 16:18:26 2013 LDS [...] cpan.org - Status changed from 'open' to 'resolved'