made it possible for a standaloneJob to provide Runnables with a functional worker_temp_directory()

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -534,11 +534,35 @@ sub debug {
 =cut
 
 sub worker_temp_directory {
-  my $self = shift;
-  return undef unless($self->worker);
-  return $self->worker->worker_process_temp_directory;
+    my $self = shift @_;
+
+        # TODO: simplify $holding_object=$self when -compile_module_once becomes the only option:
+    my $holding_object = $self->worker ? $self->worker : $self;
+
+    unless(defined($holding_object->{'_tmp_dir'}) and (-e $holding_object->{'_tmp_dir'})) {
+        my $username = $ENV{'USER'};
+        my $worker_id = $self->worker ? $self->worker->dbID : 'standalone';
+        $holding_object->{'_tmp_dir'} = "/tmp/worker_${username}.${worker_id}/";
+        mkdir($holding_object->{'_tmp_dir'}, 0777);
+        throw("unable to create a writable directory ".$holding_object->{'_tmp_dir'}) unless(-w $holding_object->{'_tmp_dir'});
+    }
+    return $holding_object->{'_tmp_dir'};
 }
 
+
+sub cleanup_worker_temp_directory {
+    my $self = shift @_;
+
+        # TODO: simplify $holding_object=$self when -compile_module_once becomes the only option:
+    my $holding_object = $self->worker ? $self->worker : $self;
+
+    if($holding_object->{'_tmp_dir'}) {
+        my $cmd = "rm -r ". $holding_object->{'_tmp_dir'};
+        system($cmd);
+    }
+}
+
+
 #################################################
 #
 # methods to make porting from RunnableDB easier

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -454,21 +454,6 @@ sub toString {
 }
 
 
-sub worker_process_temp_directory {
-  my $self = shift;
-  
-  unless(defined($self->{'_tmp_dir'}) and (-e $self->{'_tmp_dir'})) {
-    #create temp directory to hold fasta databases
-    my $username = $ENV{'USER'};
-    my $worker_id = $self->dbID;
-    $self->{'_tmp_dir'} = "/tmp/worker_${username}.${worker_id}/";
-    mkdir($self->{'_tmp_dir'}, 0777);
-    throw("unable to create a writable directory ".$self->{'_tmp_dir'}) unless(-w $self->{'_tmp_dir'});
-  }
-  return $self->{'_tmp_dir'};
-}
-
-
 sub cleanup_worker_process_temp_directory {
   my $self = shift;
   if($self->{'_tmp_dir'}) {
@@ -589,10 +574,14 @@ sub run {
 
   } while (!$self->cause_of_death); # /Worker's lifespan loop
 
-  if($self->perform_cleanup) {
-    #have runnable cleanup any global/process files/data it may have created
-    $self->cleanup_worker_process_temp_directory;
-  }
+        # have runnable clean up any global/process files/data it may have created
+    if($self->perform_cleanup) {
+        if(my $runnable_object = $self->runnable_object()) {    # if -compile_module_once is 1, keep _tmp_dir in the Process object:
+            $runnable_object->cleanup_worker_temp_directory();
+        } else {                                                # otherwise keep _tmp_dir in the Worker object, so it needs its own cleanup method:
+            $self->cleanup_worker_process_temp_directory();     #   TODO: remove this method when -compile_module_once becomes the only option
+        }
+    }
 
   $self->queen->register_worker_death($self);
 

scripts/standaloneJob.pl

@@ -10,7 +10,7 @@ use Bio::EnsEMBL::Hive::Utils ('script_usage', 'load_file_or_module', 'parse_cmd
 
 use Data::Dumper;
 
-my ($reg_conf, $help, $debug, $no_write, $flow_into, $input_id);
+my ($reg_conf, $help, $debug, $no_write, $no_cleanup, $flow_into, $input_id);
 
 my $module_or_file = shift @ARGV or script_usage();
 
@@ -19,6 +19,7 @@ GetOptions(
            'debug=i'            => \$debug,
            'reg_conf|regfile=s' => \$reg_conf,
            'no_write|nowrite'   => \$no_write,
+           'no_cleanup'         => \$no_cleanup,
            'flow_into|flow=s'   => \$flow_into,
            'input_id=s'         => \$input_id,
 );
@@ -64,6 +65,10 @@ $runnable_object->execute_writes( not $no_write );
 
 $runnable_object->life_cycle();
 
+unless($no_cleanup) {
+    $runnable_object->cleanup_worker_temp_directory();
+}
+
 __DATA__
 
 =pod