Commit a27cac4b authored by Leo Gordon's avatar Leo Gordon
Browse files

track insert_ids of separate commands and make them available for dataflow

parent 959a679e
......@@ -91,16 +91,9 @@ sub fetch_input {
? $self->db->get_AnalysisDataAdaptor->fetch_by_dbID( $self->param('did') )
: die "Could not find the command defined in input_id(), param('sql') or param('did')";
# Perform parameter substitution:
# Store the sql command array:
#
my @substituted_sqls = ();
foreach my $unsubst ((ref($sql) eq 'ARRAY') ? @$sql : ($sql) ) {
push @substituted_sqls, $self->param_substitute($unsubst);
}
# Store the substituted sql command array
#
$self->param('sqls', \@substituted_sqls);
$self->param('sqls', (ref($sql) eq 'ARRAY') ? $sql : [$sql] );
# Use connection parameters to another database if supplied, otherwise use the current database as default:
#
......@@ -126,20 +119,37 @@ sub run {
my $dbc = $self->param('dbc');
my $sqls = $self->param('sqls');
my %output_id;
# What would be a generic way of indicating an error in (My)SQL statement, that percolates through PerlDBI?
foreach my $sql (@$sqls) {
my $counter = 0;
foreach my $unsubst_sql (@$sqls) {
# Perform parameter substitution:
my $sql = $self->param_substitute($unsubst_sql);
$dbc->do( $sql );
my $insert_id_name = '_insert_id_'.$counter++;
my $insert_id_value = $dbc->db_handle->{'mysql_insertid'};
$output_id{$insert_id_name} = $insert_id_value;
$self->param($insert_id_name, $insert_id_value); # for templates
}
$self->param('output_id', \%output_id);
}
=head2 write_output
Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution.
Here we have nothing to do, as the wrapper is very generic.
Here we only flow out the insert_ids.
=cut
sub write_output {
my $self = shift;
$self->dataflow_output_id( $self->param('output_id'), 2);
}
1;
......
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