[med-svn] [gbrowse] 01/05: Remove duplicated file which is also available in libbio-perl-perl
Andreas Tille
tille at debian.org
Fri Sep 15 21:48:09 UTC 2017
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tille pushed a commit to branch master
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commit d9f170a1adafe201ad4c9a69befeaa9933be6495
Author: Andreas Tille <tille at debian.org>
Date: Fri Jan 20 21:17:30 2017 +0100
Remove duplicated file which is also available in libbio-perl-perl
---
debian/changelog | 7 +
debian/patches/remove_copy_of_LoadHelper.pm.patch | 208 ++++++++++++++++++++++
debian/patches/series | 1 +
3 files changed, 216 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index e20eb80..8256eb6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+gbrowse (2.56+dfsg-2) unstable; urgency=medium
+
+ * Remove duplicated file which is also available in libbio-perl-perl
+ Closes: #851999
+
+ -- Andreas Tille <tille at debian.org> Fri, 20 Jan 2017 18:22:41 +0100
+
gbrowse (2.56+dfsg-1) unstable; urgency=medium
[ Olivier Sallou ]
diff --git a/debian/patches/remove_copy_of_LoadHelper.pm.patch b/debian/patches/remove_copy_of_LoadHelper.pm.patch
new file mode 100644
index 0000000..8025bce
--- /dev/null
+++ b/debian/patches/remove_copy_of_LoadHelper.pm.patch
@@ -0,0 +1,208 @@
+Description: Remove duplicated file which is also available in libbio-perl-perl
+Bug-Debian: https://bugs.debian.org/851999
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 20 Jan 2017 18:22:41 +0100
+
+--- a/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
++++ /dev/null
+@@ -1,200 +0,0 @@
+-package Bio::DB::SeqFeature::Store::LoadHelper;
+-
+-# NOTE: This overwrites the version in bioperl-live!!
+-
+-=head1 NAME
+-
+-Bio::DB::SeqFeature::Store::LoadHelper -- Internal utility for Bio::DB::SeqFeature::Store
+-
+-=head1 SYNOPSIS
+-
+- # For internal use only.
+-
+-=head1 DESCRIPTION
+-
+-For internal use only
+-
+-=head1 SEE ALSO
+-
+-L<bioperl>,
+-L<Bio::DB::SeqFeature::Store>,
+-L<Bio::DB::SeqFeature::Segment>,
+-L<Bio::DB::SeqFeature::NormalizedFeature>,
+-L<Bio::DB::SeqFeature::GFF2Loader>,
+-L<Bio::DB::SeqFeature::Store::DBI::mysql>,
+-L<Bio::DB::SeqFeature::Store::berkeleydb>
+-
+-=head1 AUTHOR
+-
+-Lincoln Stein E<lt>lstein at cshl.orgE<gt>.
+-
+-Copyright (c) 2006 Cold Spring Harbor Laboratory.
+-
+-This library is free software; you can redistribute it and/or modify
+-it under the same terms as Perl itself.
+-
+-=cut
+-
+-use strict;
+-use DB_File;
+-use File::Path 'rmtree';
+-use File::Temp 'tempdir';
+-use File::Spec;
+-use Fcntl qw(O_CREAT O_RDWR);
+-
+-our $VERSION = '1.10';
+-
+-my %DBHandles;
+-
+-sub new {
+- my $class = shift;
+- my $tmpdir = shift;
+-
+- my $template = 'SeqFeatureLoadHelper_XXXXXX';
+-
+- my @tmpargs = $tmpdir ? ($template,DIR=>$tmpdir) : ($template);
+- my $tmppath = tempdir(@tmpargs,CLEANUP=>1);
+- my $self = $class->create_dbs($tmppath);
+- $self->{tmppath} = $tmppath;
+- return bless $self,$class;
+-}
+-
+-sub DESTROY {
+- my $self = shift;
+- rmtree $self->{tmppath};
+-# File::Temp::cleanup() unless $self->{keep};
+-}
+-
+-sub create_dbs {
+- my $self = shift;
+- my $tmp = shift;
+- my %self;
+- # experiment with caching these handles in memory
+- my $hash_options = DB_File::HASHINFO->new();
+- # Each of these hashes allow only unique keys
+- for my $dbname (qw(IndexIt TopLevel Local2Global)) {
+- unless ($DBHandles{$dbname}) {
+- my %h;
+- tie(%h,'DB_File',File::Spec->catfile($tmp,$dbname),
+- O_CREAT|O_RDWR,0666,$hash_options);
+- $DBHandles{$dbname} = \%h;
+- }
+- $self{$dbname} = $DBHandles{$dbname};
+- %{$self{$dbname}} = ();
+- }
+-
+- # The Parent2Child hash allows duplicate keys, so we
+- # create it with the R_DUP flag.
+- my $btree_options = DB_File::BTREEINFO->new();
+- $btree_options->{flags} = R_DUP;
+- unless ($DBHandles{'Parent2Child'}) {
+- my %h;
+- tie(%h,'DB_File',File::Spec->catfile($tmp,'Parent2Child'),
+- O_CREAT|O_RDWR,0666,$btree_options);
+- $DBHandles{'Parent2Child'} = \%h;
+- }
+- $self{Parent2Child} = $DBHandles{'Parent2Child'};
+- %{$self{Parent2Child}} = ();
+- return \%self;
+-}
+-
+-sub indexit {
+- my $self = shift;
+- my $id = shift;
+- $self->{IndexIt}{$id} = shift if @_;
+- return $self->{IndexIt}{$id};
+-}
+-
+-sub toplevel {
+- my $self = shift;
+- my $id = shift;
+- $self->{TopLevel}{$id} = shift if @_;
+- return $self->{TopLevel}{$id};
+-}
+-
+-sub each_toplevel {
+- my $self = shift;
+- my ($id) = each %{$self->{TopLevel}};
+- $id;
+-}
+-
+-sub local2global {
+- my $self = shift;
+- my $id = shift;
+- $self->{Local2Global}{$id} = shift if @_;
+- return $self->{Local2Global}{$id};
+-}
+-
+-sub add_children {
+- my $self = shift;
+- my $parent_id = shift;
+- # (@children) = @_;
+- $self->{Parent2Child}{$parent_id} = shift while @_;
+-}
+-
+-sub children {
+- my $self = shift;
+- my $parent_id = shift;
+-
+- my @children;
+-
+- my $db = tied(%{$self->{Parent2Child}});
+- my $key = $parent_id;
+- my $value = '';
+- for (my $status = $db->seq($key,$value,R_CURSOR);
+- $status == 0 && $key eq $parent_id;
+- $status = $db->seq($key,$value,R_NEXT)
+- ) {
+- push @children,$value;
+- }
+- return wantarray ? @children: \@children;
+-}
+-
+-# this acts like each() and returns each parent id and an array ref of children
+-sub each_family {
+- my $self = shift;
+-
+- my $db = tied(%{$self->{Parent2Child}});
+-
+- if ($self->{_cursordone}) {
+- undef $self->{_cursordone};
+- undef $self->{_parent};
+- undef $self->{_child};
+- return;
+- }
+-
+- # do a slightly tricky cursor search
+- unless (defined $self->{_parent}) {
+- return unless $db->seq($self->{_parent},$self->{_child},R_FIRST) == 0;
+- }
+-
+- my $parent = $self->{_parent};
+- my @children = $self->{_child};
+-
+- my $status;
+- while (($status = $db->seq($self->{_parent},$self->{_child},R_NEXT)) == 0
+- && $self->{_parent} eq $parent
+- ) {
+- push @children,$self->{_child};
+- }
+-
+- $self->{_cursordone}++ if $status != 0;
+-
+- return ($parent,\@children);
+-}
+-
+-sub local_ids {
+- my $self = shift;
+- my @ids = keys %{$self->{Local2Global}}
+- if $self->{Local2Global};
+- return \@ids;
+-}
+-
+-sub loaded_ids {
+- my $self = shift;
+- my @ids = values %{$self->{Local2Global}}
+- if $self->{Local2Global};
+- return \@ids;
+-}
+-
+-1;
diff --git a/debian/patches/series b/debian/patches/series
index d840f87..f6bb9d9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -8,3 +8,4 @@ init_script_dependency.patch
fix_runlevel.patch
spelling.patch
fix_whatis_entry.patch
+remove_copy_of_LoadHelper.pm.patch
--
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