new calculation of avg_msec_per_job

better debug system to allow worker to control analysis debug level
new batch_size method will use avg_msec_per_job to calculate batch_size on the fly
  if analysis_stat.batch_size==0

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -73,6 +73,7 @@ use strict;
 use Bio::EnsEMBL::Utils::Argument;
 use Bio::EnsEMBL::Utils::Exception;
 use Sys::Hostname;
+use Time::HiRes qw(time);
 
 use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::DBSQL::DBAdaptor;
@@ -91,6 +92,7 @@ sub new {
 sub init {
   my $self = shift;
   $self->{'start_time'} = time();
+  $self->debug(0);
   return $self;
 }
 
@@ -109,6 +111,12 @@ sub beekeeper {
   $self->{'_beekeeper'} = shift if(@_);
   return $self->{'_beekeeper'};
 }
+sub debug {
+  my $self = shift;
+  $self->{'_debug'} = shift if(@_);
+  $self->{'_debug'}=0 unless(defined($self->{'_debug'}));
+  return $self->{'_debug'};
+}
 
 =head2 analysis
 
@@ -250,6 +258,13 @@ sub output_dir {
   return $self->{'_output_dir'};
 }
 
+sub perform_global_cleanup {
+  my $self = shift;
+  $self->{'_perform_global_cleanup'} = shift if(@_);
+  $self->{'_perform_global_cleanup'} = 1 unless(defined($self->{'_perform_global_cleanup'}));
+  return $self->{'_perform_global_cleanup'};
+}
+
 sub print_worker {
   my $self = shift;
   print("WORKER: hive_id=",$self->hive_id,
@@ -271,7 +286,7 @@ sub print_worker {
 
 =head2 batch_size
 
-  Arg [1] : (optional) string $value
+  Args    :   none
   Title   :   batch_size
   Usage   :   $value = $self->batch_size;
               $self->batch_size($new_value);
@@ -287,13 +302,19 @@ sub print_worker {
 sub batch_size {
   my $self = shift;
   
+  my $stats = $self->analysis->stats;
+  my $batch_size = $stats->batch_size;
   if(@_) {
-    my $batch_size = shift;
-    my $stats = $self->analysis->stats;
+    $batch_size = shift;
     $stats->batch_size($batch_size);
     $stats->update;
+  }  
+  
+  if(($batch_size == 0) and ($stats->avg_msec_per_job)) {
+    $batch_size = int(15000 / $stats->avg_msec_per_job); # num jobs in 15 secs
   }
-  my $batch_size = $self->analysis->stats->batch_size;
+  $batch_size = 1 if($batch_size < 1); # make sure we grab at least one job
+  
   if($self->job_limit and ($self->job_limit < $batch_size)) {
     $batch_size = $self->job_limit;
   }
@@ -342,6 +363,8 @@ sub run
   $self->db->dbc->disconnect_when_inactive(0);
 
   my $jobDBA = $self->db->get_AnalysisJobAdaptor;
+  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
+
   my $alive=1;  
   while($alive) {
     my $jobs = [];
@@ -353,11 +376,14 @@ sub run
       $jobs = $jobDBA->fetch_by_claim_analysis($claim, $self->analysis->dbID);
     }
 
-    $self->queen->worker_check_in($self);
+    $self->queen->worker_check_in($self); #will sync analysis_stats if >60sec overdue
 
     $self->cause_of_death('NO_WORK') unless(scalar @{$jobs});
 
-    print(STDOUT "claimed ",scalar(@{$jobs}), " jobs to process\n");
+    $self->analysis->stats->print_stats if($self->debug);
+    print(STDOUT "claimed ",scalar(@{$jobs}), " jobs to process\n") if($self->debug);
+    
+    my $batch_start = time() * 1000;    
     foreach my $job (@{$jobs}) {
       $self->redirect_job_output($job);
       $self->run_module_with_job($job);
@@ -366,6 +392,11 @@ sub run
       $self->close_and_update_job_output($job);
       $self->{'_work_done'}++;
     }
+    my $batch_end = time() * 1000;
+    #printf("batch start:%f end:%f\n", $batch_start, $batch_end);
+    $statsDBA->interval_update_work_done($self->analysis->dbID, 
+                                         scalar(@$jobs), 
+                                         ($batch_end - $batch_start));
 
     $self->cause_of_death('JOB_LIMIT') if($specific_job);
 
@@ -381,8 +412,11 @@ sub run
     #}
     if($self->cause_of_death) { $alive=undef; }
   }
-  #have runnable cleanup any global/process files/data it may have created
-  $self->analysis->runnableDB->global_cleanup();
+  
+  if($self->perform_global_cleanup) {
+    #have runnable cleanup any global/process files/data it may have created
+    $self->analysis->runnableDB->global_cleanup();
+  }
 
   $self->queen->register_worker_death($self);
 
@@ -412,6 +446,7 @@ sub run_module_with_job
   #pass the input_id from the job into the runnableDB object
   $runObj->input_id($job->input_id);
   $runObj->analysis_job_id($job->dbID);
+  $runObj->debug($self->debug);
   
   $job->status('GET_INPUT');
   $runObj->fetch_input;