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The Basics
Id: 44098
Status: resolved
Priority: 0/
Queue: onto-perl

People
Owner: Nobody in particular
Requestors: jouni.valiaho [...] uta.fi
Cc:
AdminCc:

Bug Information
Severity: Normal
Broken in: 1.13
Fixed in: (no value)



Subject: No export for obo relationships
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perl version: v5.10.0 operation system: Linux fm2pc74 2.6.27.19-170.2.35.fc10.i686 #1 SMP The export function does not export relationships as in obo format (probably not in other formats as well, not tested). The attachment contains a patch proposal, that fixes the bug for obo format and adds the export function for missing saved-by parameter.
Subject: patch.Ontology.pm
Download patch.Ontology.pm
text/x-perl 2.2k
--- OBO/Core/Ontology.pm 2009-03-13 12:59:30.000000000 +0200 +++ OBO/Core/Ontology.pm.new 2009-03-13 12:58:26.000000000 +0200 @@ -1259,9 +1259,9 @@ my @heads; if ($element && $relationship_type) { my @rels = values(%{$self->{SOURCE_RELATIONSHIPS}->{$element}}); - my $relationship_type_id = $relationship_type->id(); +# my $relationship_type_id = $relationship_type->id(); foreach my $rel (@rels) { - push @heads, $rel->head() if ($rel->type() eq $relationship_type_id); + push @heads, $rel->head() if ($rel->type() eq $relationship_type->name()); } } return \@heads; @@ -1383,6 +1383,8 @@ print $file_handle "format-version: 1.2\n"; chomp(my $local_date = __date()); # `date '+%d:%m:%Y %H:%M'` # date: 11:05:2008 12:52 print $file_handle "date: ", (defined $self->date())?$self->date():$local_date, "\n"; + my $saved_by = $self->saved_by(); + print $file_handle "saved-by: ", $saved_by, "\n" if (defined $saved_by); print $file_handle "auto-generated-by: ONTO-PERL\n"; # import @@ -1501,7 +1503,7 @@ # # is_a: # - my $rt = $self->get_relationship_type_by_id("is_a"); + my $rt = $self->get_relationship_type_by_name("is_a"); if (defined $rt) { my %saw_is_a; # avoid duplicated arrows (RelationshipSet?) my @heads = @{$self->get_head_by_relationship_type($term, $rt)}; @@ -1542,13 +1544,13 @@ my %saw1; # foreach $rt (sort {lc($a->id()) cmp lc($b->id())} @{$self->get_relationship_types()}) { foreach $rt (grep (!$saw1{$_}++, sort {lc($a->id()) cmp lc($b->id())} @{$self->get_relationship_types()})) { # use this foreach-line if there are duplicated rel's - my $rt_id = $rt->id(); - if ($rt_id ne "is_a") { # is_a is printed above + my $rt_name = $rt->name(); + if ($rt_name ne "is_a") { # is_a is printed above my @heads = @{$self->get_head_by_relationship_type($term, $rt)}; my %saw2; #foreach my $head (sort {lc($a->id()) cmp lc($b->id())} @heads) { foreach my $head (grep (!$saw2{$_}++, sort {lc($a->id()) cmp lc($b->id())} @heads)) { # use this foreach-line if there are duplicated rel's - print $file_handle "\nrelationship: ", $rt_id, " ", $head->id(), " ! ", $head->name(); + print $file_handle "\nrelationship: ", $rt_name, " ", $head->id(), " ! ", $head->name(); } } }
are you still facing the issue you reported "some time ago"?
Issue fixed...


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