Commit 6fd5baf6 authored by Magali Ruffier's avatar Magali Ruffier
Browse files

arrays/hashes updates

parent 03d4a97c
......@@ -19,8 +19,8 @@ sub run {
}
my $helper = $dba->dbc()->sql_helper();
my %attrib_codes = $self->get_attrib_codes();
$self->delete_old_attrib($dba, %attrib_codes);
my @attrib_codes = $self->get_attrib_codes();
$self->delete_old_attrib($dba, @attrib_codes);
my $tmpfile = $self->param('tmpdir') . "/$$.pep";
$self->dump_translation($dba, $tmpfile);
......@@ -39,12 +39,24 @@ sub store_attrib {
my $prod_dba = $self->get_production_DBAdaptor();
my $prod_helper = $prod_dba->dbc()->sql_helper();
my @attribs;
my $sql = q{
SELECT name, description
my $sqlName = q{
SELECT name
FROM attrib_type
WHERE code = ? };
my $sqlDesc = q{
SELECT description
FROM attrib_type
WHERE code = ? };
foreach my $key (keys %$results) {
my ($name, $description) = $prod_helper->execute(-SQL => $sql, -PARAMS => [$key]);
my ($name, $description);
my @names = @{ $prod_helper->execute_simple(-SQL => $sqlName, -PARAMS => [$key]) };
foreach my $bit (@names) {
$name .= $bit . " ";
}
my @descriptions = @{ $prod_helper->execute_simple(-SQL => $sqlDesc, -PARAMS => [$key]) };
foreach my $bit (@descriptions) {
$description .= $bit . " ";
}
my $value = $results->{$key};
my $attrib = Bio::EnsEMBL::Attribute->new(
-NAME => $name,
......@@ -86,7 +98,7 @@ sub run_pepstats {
sub delete_old_attrib {
my ($self, $dba, %attrib_codes) = @_;
my ($self, $dba, @attrib_codes) = @_;
my $helper = $dba->dbc()->sql_helper();
my $sql = q{
DELETE ta
......@@ -98,8 +110,8 @@ sub delete_old_attrib {
AND s.coord_system_id = c.coord_system_id
AND c.species_id = ?
AND at.code = ? };
foreach my $key (keys %attrib_codes) {
$helper->execute_update(-SQL => $sql, -PARAMS => [$dba->species_id(), $key]) ;
foreach my $code (@attrib_codes) {
$helper->execute_update(-SQL => $sql, -PARAMS => [$dba->species_id(), $code]) ;
}
}
......@@ -109,11 +121,11 @@ sub get_attrib_codes {
my $prod_dba = $self->get_production_DBAdaptor();
my $prod_helper = $prod_dba->dbc()->sql_helper();
my $sql = q{
SELECT code, name
SELECT code
FROM attrib_type
WHERE description = 'Pepstats attributes' };
my %attrib_codes = %{ $prod_helper->execute_into_hash(-SQL => $sql) };
return %attrib_codes;
my @attrib_codes = @{ $prod_helper->execute_simple(-SQL => $sql) };
return @attrib_codes;
}
......
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