bugfix: make sure we pause the timer to avoid accumulating running totals

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -139,18 +139,18 @@ sub life_cycle {
     $self->enter_status('FETCH_INPUT');
     $partial_stopwatch->restart();
     $self->fetch_input;
-    $job_partial_timing{'FETCH_INPUT'} = $partial_stopwatch->get_elapsed();
+    $job_partial_timing{'FETCH_INPUT'} = $partial_stopwatch->pause->get_elapsed;
 
     $self->enter_status('RUN');
     $partial_stopwatch->restart();
     $self->run;
-    $job_partial_timing{'RUN'} = $partial_stopwatch->get_elapsed();
+    $job_partial_timing{'RUN'} = $partial_stopwatch->pause->get_elapsed;
 
     if($self->execute_writes) {
         $self->enter_status('WRITE_OUTPUT');
         $partial_stopwatch->restart();
         $self->write_output;
-        $job_partial_timing{'WRITE_OUTPUT'} = $partial_stopwatch->get_elapsed();
+        $job_partial_timing{'WRITE_OUTPUT'} = $partial_stopwatch->pause->get_elapsed;
 
         if( $job->autoflow ) {
             print STDERR "\njob ".$job->dbID." : AUTOFLOW input->output\n" if($self->debug);

modules/Bio/EnsEMBL/Hive/Utils/Stopwatch.pm

@@ -63,7 +63,7 @@ sub new {
     return $self;
 }
 
-sub _unit {             # only set it once for each timer to avoid messing everything up
+sub _unit {                 # only set it once for each timer to avoid messing everything up
     my $self = shift;
 
     $self->{'_unit'} = shift if(@_);
@@ -84,24 +84,25 @@ sub accumulated {
     return $self->{'_accumulated'} || 0;
 }
 
-sub continue {
+sub continue {              # the opposite of pause()
     my $self = shift @_;
 
     unless($self->is_counting) {    # ignore if it was already running
         $self->is_counting(1);
         $self->{'_start'} = time() * $self->_unit
     }
+
+    return $self;
 }
 
 sub restart {
     my $self = shift @_;
 
     $self->accumulated(0);
-    $self->continue;
-    return $self;
+    return $self->continue;
 }
 
-sub get_elapsed {       # peek without stopping (in case it was running)
+sub get_elapsed {           # peek without stopping (in case it was running)
     my $self = shift @_;
 
     return ($self->accumulated + $self->is_counting * (time() * $self->_unit - $self->{'_start'}));
@@ -112,6 +113,8 @@ sub pause {
 
     $self->accumulated( $self->get_elapsed );
     $self->is_counting(0);
+
+    return $self;
 }
 
 1;