Andreas Tille pushed to branch master at Debian Med / libbio-db-seqfeature-perl
Commits: 6bc2b7f5 by Andreas Tille at 2025-11-04T14:45:46+01:00 * Fix "Column name offset is a reserved word in mysql" Closes: #1120035 - - - - - 3 changed files: - debian/changelog - + debian/patches/c78ba356bbd015ba7e0ee119754b198037593821.patch - + debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +libbio-db-seqfeature-perl (1.7.5-2) UNRELEASED; urgency=medium + + * Team upload. + + [ Moritz Schlarb ] + * Fix "Column name offset is a reserved word in mysql" + Closes: #1120035 + + -- Andreas Tille <[email protected]> Tue, 04 Nov 2025 14:29:17 +0100 + libbio-db-seqfeature-perl (1.7.5-1) unstable; urgency=medium * New upstream version 1.7.5 ===================================== debian/patches/c78ba356bbd015ba7e0ee119754b198037593821.patch ===================================== @@ -0,0 +1,88 @@ +From: Moritz Schlarb <[email protected]> +Origin: https://github.com/bioperl/Bio-DB-SeqFeature/pull/6/commits/c78ba356bbd015ba7e0ee119754b198037593821 +Last-Update: 2025-11-04 +Bug-Debian: https://bugs.debian.org/1120035 +Subject: [PATCH] Fix "Column name offset is a reserved word in mysql" + +Closes #5 +--- + lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm | 12 ++++++------ + lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm | 12 ++++++------ + 2 files changed, 12 insertions(+), 12 deletions(-) + +diff --git a/lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm b/lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm +index 070c9c1..96ac1b7 100644 +--- a/lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm ++++ b/lib/Bio/DB/SeqFeature/Store/DBI/MariaDB.pm +@@ -315,9 +315,9 @@ END + sequence => <<END, + ( + id int(10) not null, +- offset int(10) unsigned not null, ++ `offset` int(10) unsigned not null, + sequence longblob, +- primary key(id,offset) ++ primary key(id,`offset`) + ) + END + interval_stats => <<END, +@@ -684,7 +684,7 @@ sub _fetch_sequence { + my $sequence_table = $self->_sequence_table; + + my $sql = <<END; +-SELECT sequence,offset ++SELECT sequence,s.offset + FROM $sequence_table as s + WHERE s.id=? + AND s.offset >= ? +@@ -718,9 +718,9 @@ sub _offset_boundary { + my $locationlist_table = $self->_locationlist_table; + + my $sql; +- $sql = $position eq 'left' ? "SELECT min(offset) FROM $sequence_table as s WHERE s.id=?" +- :$position eq 'right' ? "SELECT max(offset) FROM $sequence_table as s WHERE s.id=?" +- :"SELECT max(offset) FROM $sequence_table as s WHERE s.id=? AND offset<=?"; ++ $sql = $position eq 'left' ? "SELECT min(s.offset) FROM $sequence_table as s WHERE s.id=?" ++ :$position eq 'right' ? "SELECT max(s.offset) FROM $sequence_table as s WHERE s.id=?" ++ :"SELECT max(s.offset) FROM $sequence_table as s WHERE s.id=? AND s.offset<=?"; + my $sth = $self->_prepare($sql); + my @args = $position =~ /^-?\d+$/ ? ($seqid,$position) : ($seqid); + $self->_print_query($sql,@args) if DEBUG || $self->debug; +diff --git a/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm b/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm +index a92aff0..8338f34 100644 +--- a/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm ++++ b/lib/Bio/DB/SeqFeature/Store/DBI/mysql.pm +@@ -315,9 +315,9 @@ END + sequence => <<END, + ( + id int(10) not null, +- offset int(10) unsigned not null, ++ `offset` int(10) unsigned not null, + sequence longblob, +- primary key(id,offset) ++ primary key(id,`offset`) + ) + END + interval_stats => <<END, +@@ -684,7 +684,7 @@ sub _fetch_sequence { + my $sequence_table = $self->_sequence_table; + + my $sql = <<END; +-SELECT sequence,offset ++SELECT sequence,s.offset + FROM $sequence_table as s + WHERE s.id=? + AND s.offset >= ? +@@ -718,9 +718,9 @@ sub _offset_boundary { + my $locationlist_table = $self->_locationlist_table; + + my $sql; +- $sql = $position eq 'left' ? "SELECT min(offset) FROM $sequence_table as s WHERE s.id=?" +- :$position eq 'right' ? "SELECT max(offset) FROM $sequence_table as s WHERE s.id=?" +- :"SELECT max(offset) FROM $sequence_table as s WHERE s.id=? AND offset<=?"; ++ $sql = $position eq 'left' ? "SELECT min(s.offset) FROM $sequence_table as s WHERE s.id=?" ++ :$position eq 'right' ? "SELECT max(s.offset) FROM $sequence_table as s WHERE s.id=?" ++ :"SELECT max(s.offset) FROM $sequence_table as s WHERE s.id=? AND s.offset<=?"; + my $sth = $self->_prepare($sql); + my @args = $position =~ /^-?\d+$/ ? ($seqid,$position) : ($seqid); + $self->_print_query($sql,@args) if DEBUG || $self->debug; ===================================== debian/patches/series ===================================== @@ -0,0 +1 @@ +c78ba356bbd015ba7e0ee119754b198037593821.patch View it on GitLab: https://salsa.debian.org/med-team/libbio-db-seqfeature-perl/-/commit/6bc2b7f50c1773a7af7bcec263b667f68bcbb877 -- View it on GitLab: https://salsa.debian.org/med-team/libbio-db-seqfeature-perl/-/commit/6bc2b7f50c1773a7af7bcec263b667f68bcbb877 You're receiving this email because of your account on salsa.debian.org.
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