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Commit ecc57d45 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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We made exceptions for the cases where the BaseMetaContainer class was 

inherited and used by the Variation, Funcgen, or Compara APIs, because
these other schemas didn't use to have a species_id column in their meta
tables.  Now they do, so we're removing the exceptions.
parent e57f4250
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modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
+ 51
− 76
View file @ ecc57d45
......@@ -109,26 +109,20 @@ sub list_value_by_key {
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
if ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( "SELECT meta_value "
. "FROM meta "
. "WHERE meta_key = ? "
. "ORDER BY meta_id" );
} elsif ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( "SELECT meta_value "
. "FROM meta "
. "WHERE meta_key = ? "
. "AND species_id IS NULL "
. "ORDER BY meta_id" );
$self->prepare( "SELECT meta_value "
. "FROM meta "
. "WHERE meta_key = ? "
. "AND species_id IS NULL "
. "ORDER BY meta_id" );
} else {
$sth =
$self->prepare( "SELECT meta_value "
. "FROM meta "
. "WHERE meta_key = ? "
. "AND species_id = ? "
. "ORDER BY meta_id" );
$self->prepare( "SELECT meta_value "
. "FROM meta "
. "WHERE meta_key = ? "
. "AND species_id = ? "
. "ORDER BY meta_id" );
$sth->bind_param( 2, $self->species_id(), SQL_INTEGER );
}
......@@ -173,17 +167,14 @@ sub store_key_value {
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth = $self->prepare(
'INSERT INTO meta (meta_key, meta_value) VALUES(?, ?)');
} elsif ( !$self->_species_specific_key($key) ) {
if ( !$self->_species_specific_key($key) ) {
$sth = $self->prepare(
'INSERT INTO meta (meta_key, meta_value, species_id) '
. 'VALUES(?, ?, \N)' );
'INSERT INTO meta (meta_key, meta_value, species_id) '
. 'VALUES(?, ?, \N)' );
} else {
$sth = $self->prepare(
'INSERT INTO meta (meta_key, meta_value, species_id) '
. 'VALUES (?, ?, ?)' );
'INSERT INTO meta (meta_key, meta_value, species_id) '
. 'VALUES (?, ?, ?)' );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
}
......@@ -216,20 +207,17 @@ sub update_key_value {
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth = $self->prepare(
'UPDATE meta SET meta_value = ? WHERE meta_key = ?' );
} elsif ( !$self->_species_specific_key($key) ) {
if ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'UPDATE meta SET meta_value = ? '
. 'WHERE meta_key = ?'
. 'AND species_id IS NULL' );
$self->prepare( 'UPDATE meta SET meta_value = ? '
. 'WHERE meta_key = ?'
. 'AND species_id IS NULL' );
} else {
$sth =
$self->prepare( 'UPDATE meta '
. 'SET meta_value = ? '
. 'WHERE meta_key = ? '
. 'AND species_id = ?' );
$self->prepare( 'UPDATE meta '
. 'SET meta_value = ? '
. 'WHERE meta_key = ? '
. 'AND species_id = ?' );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
}
......@@ -259,18 +247,16 @@ sub delete_key {
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth = $self->prepare( 'DELETE FROM meta WHERE meta_key = ?' );
} elsif ( !$self->_species_specific_key($key) ) {
if ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ?'
. 'AND species_id IS NULL' );
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ?'
. 'AND species_id IS NULL' );
} else {
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND species_id = ?' );
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND species_id = ?' );
$sth->bind_param( 2, $self->species_id(), SQL_INTEGER );
}
......@@ -301,23 +287,18 @@ sub delete_key_value {
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
if ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?' );
} elsif ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?'
. 'AND species_id IS NULL' );
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?'
. 'AND species_id IS NULL' );
} else {
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ? '
. 'AND species_id = ?' );
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ? '
. 'AND species_id = ?' );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
}
......@@ -349,26 +330,20 @@ sub key_value_exists {
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth =
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?' );
} elsif ( !$self->_species_specific_key($key) ) {
if ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?'
. 'AND species_id IS NULL' );
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?'
. 'AND species_id IS NULL' );
} else {
$sth =
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ? '
. 'AND species_id = ?' );
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ? '
. 'AND species_id = ?' );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
}
......
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