Commit 192f4078 authored by Leo Gordon's avatar Leo Gordon
Browse files

allow a non-process to enjoy dataflow mechanism - just because it has become possible

parent d5c63e99
...@@ -639,29 +639,29 @@ sub run_module_with_job { ...@@ -639,29 +639,29 @@ sub run_module_with_job {
my ($self, $job) = @_; my ($self, $job) = @_;
$job->incomplete(1); $job->incomplete(1);
$job->autoflow(1);
$self->enter_status('COMPILATION'); $self->enter_status('COMPILATION');
$job->update_status('COMPILATION'); $job->update_status('COMPILATION');
my $runObj = $self->analysis->process or die "Unknown compilation error"; my $runObj = $self->analysis->process or die "Unknown compilation error";
my $native_hive_process = $runObj->isa("Bio::EnsEMBL::Hive::Process");
my $job_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new()->restart(); my $job_stopwatch = Bio::EnsEMBL::Hive::Utils::Stopwatch->new()->restart();
$self->queen->dbc->query_count(0); $self->queen->dbc->query_count(0);
#pass the input_id from the job into the Process object #pass the input_id from the job into the Process object
if($native_hive_process) { if( $runObj->isa('Bio::EnsEMBL::Hive::Process') ) {
$runObj->input_job($job); $runObj->input_job($job);
$runObj->queen($self->queen); $runObj->queen($self->queen);
$runObj->worker($self); $runObj->worker($self);
$runObj->debug($self->debug); $runObj->debug($self->debug);
$job->autoflow(1);
$job->param_init( $runObj->strict_hash_format(), $runObj->param_defaults(), $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() ); $job->param_init( $runObj->strict_hash_format(), $runObj->param_defaults(), $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() );
} else { } else {
$runObj->input_id($job->input_id); $runObj->input_id($job->input_id);
$runObj->db($self->db); $runObj->db($self->db);
$job->param_init( 0, $self->db->get_MetaContainer->get_param_hash(), $self->analysis->parameters(), $job->input_id() ); # Well, why not?
} }
$self->enter_status('GET_INPUT'); $self->enter_status('GET_INPUT');
...@@ -689,9 +689,9 @@ sub run_module_with_job { ...@@ -689,9 +689,9 @@ sub run_module_with_job {
$runObj->write_output; $runObj->write_output;
$self->{'writing_stopwatch'}->pause(); $self->{'writing_stopwatch'}->pause();
if( $native_hive_process and $job->autoflow ) { if( $job->autoflow ) {
printf("AUTOFLOW input->output\n") if($self->debug); printf("AUTOFLOW input->output\n") if($self->debug);
$runObj->dataflow_output_id(); $job->dataflow_output_id();
} }
} else { } else {
print("\n\n!!!! NOT write_output\n\n\n") if($self->debug); print("\n\n!!!! NOT write_output\n\n\n") if($self->debug);
......
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