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Commit 8289410e authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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For Compara, Funcgen, and Variation databases, do not try to access a 

species_id column in the meta table.

Unit-tests passes.
parent 1507aefa
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modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm
+ 75
− 61
View file @ 8289410e
......@@ -97,16 +97,20 @@ sub list_value_by_key {
}
my $sth;
if ( !$self->_species_specific_key($key) ) {
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$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" );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->execute();
} else {
$sth =
$self->prepare( "SELECT meta_value "
......@@ -114,12 +118,12 @@ sub list_value_by_key {
. "WHERE meta_key = ? "
. "AND species_id = ? "
. "ORDER BY meta_id" );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $self->species_id(), SQL_INTEGER );
$sth->execute();
}
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->execute();
my @result;
while ( my $arrRef = $sth->fetchrow_arrayref() ) {
push( @result, $arrRef->[0] );
......@@ -156,25 +160,26 @@ sub store_key_value {
return;
}
if ( !$self->_species_specific_key($key) ) {
my $sth = $self->prepare(
'INSERT INTO meta (species_id, meta_key, meta_value) '
. 'VALUES(\N, ?, ?)' );
my $sth;
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->execute();
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth = $self->prepare(
'INSERT INTO meta (meta_key, meta_value) VALUES(?, ?)');
} elsif ( !$self->_species_specific_key($key) ) {
$sth = $self->prepare(
'INSERT INTO meta (meta_key, meta_value, species_id) '
. 'VALUES(?, ?, \N)' );
} else {
my $sth = $self->prepare(
'INSERT INTO meta (species_id, meta_key, meta_value) '
$sth = $self->prepare(
'INSERT INTO meta (meta_key, meta_value, species_id) '
. 'VALUES (?, ?, ?)' );
$sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
$sth->bind_param( 2, $key, SQL_VARCHAR );
$sth->bind_param( 3, $value, SQL_VARCHAR );
$sth->execute();
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
}
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->execute();
$self->{'cache'} ||= {};
delete $self->{'cache'}->{$key};
......@@ -198,27 +203,29 @@ sub store_key_value {
sub update_key_value {
my ( $self, $key, $value ) = @_;
if ( !$self->_species_specific_key($key) ) {
my $sth =
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) ) {
$sth =
$self->prepare( 'UPDATE meta SET meta_value = ? '
. 'WHERE meta_key = ?'
. 'AND species_id IS NULL' );
$sth->bind_param( 1, $value, SQL_VARCHAR );
$sth->bind_param( 2, $key, SQL_VARCHAR );
$sth->execute();
} else {
my $sth =
$sth =
$self->prepare( 'UPDATE meta '
. 'SET meta_value = ? '
. 'WHERE meta_key = ? '
. 'AND species_id = ?' );
$sth->bind_param( 1, $value, SQL_VARCHAR );
$sth->bind_param( 2, $key, SQL_VARCHAR );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
$sth->execute();
}
$sth->bind_param( 1, $value, SQL_VARCHAR );
$sth->bind_param( 2, $key, SQL_VARCHAR );
$sth->execute();
} ## end sub update_key_value
......@@ -239,25 +246,26 @@ sub update_key_value {
sub delete_key {
my ( $self, $key ) = @_;
if ( !$self->_species_specific_key($key) ) {
my $sth =
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth = $self->prepare( 'DELETE FROM meta WHERE meta_key = ?' );
} elsif ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ?'
. 'AND species_id IS NULL' );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->execute();
} else {
my $sth =
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND species_id = ?' );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $self->species_id(), SQL_INTEGER );
$sth->execute();
}
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->execute();
delete $self->{'cache'}->{$key};
}
......@@ -280,29 +288,32 @@ sub delete_key {
sub delete_key_value {
my ( $self, $key, $value ) = @_;
if ( !$self->_species_specific_key($key) ) {
my $sth =
my $sth;
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$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' );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->execute();
} else {
my $sth =
$sth =
$self->prepare( 'DELETE FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ? '
. 'AND species_id = ?' );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
$sth->execute();
}
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->execute();
delete $self->{'cache'}->{$key};
} ## end sub delete_key_value
......@@ -326,17 +337,20 @@ sub key_value_exists {
my ( $self, $key, $value ) = @_;
my $sth;
if ( !$self->_species_specific_key($key) ) {
if ( ref($self) =~ /Compara|Funcgen|Variation/ ) {
$sth =
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?' );
} elsif ( !$self->_species_specific_key($key) ) {
$sth =
$self->prepare( 'SELECT meta_value '
. 'FROM meta '
. 'WHERE meta_key = ? '
. 'AND meta_value = ?'
. 'AND species_id IS NULL' );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->execute();
} else {
$sth =
$self->prepare( 'SELECT meta_value '
......@@ -344,13 +358,13 @@ sub key_value_exists {
. 'WHERE meta_key = ? '
. 'AND meta_value = ? '
. 'AND species_id = ?' );
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->bind_param( 3, $self->species_id(), SQL_INTEGER );
$sth->execute();
}
$sth->bind_param( 1, $key, SQL_VARCHAR );
$sth->bind_param( 2, $value, SQL_VARCHAR );
$sth->execute();
while ( my $arrRef = $sth->fetchrow_arrayref() ) {
if ( $arrRef->[0] eq $value ) {
$sth->finish();
......
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