added method for adjusting number of needed workers by the number of

'living' workers in the hive. Also changed the way adaptors are held
to avoid any problems of the type of DBAdaptor used to create the queen

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -65,7 +65,7 @@ use Sys::Hostname;
 our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
 
 #
-# STORE METHODS
+# PUBLIC METHODS
 #
 ################
 
@@ -83,7 +83,7 @@ our @ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
 sub create_new_worker {
   my ($self,$analysis_id) = @_;
 
-  my $analStatsDBA = $self->db->get_AnalysisStatsAdaptor;
+  my $analStatsDBA = $self->_analysisStatsAdaptor;
   return undef unless($analStatsDBA);
   
   my $analysisStats = $analStatsDBA->fetch_by_analysis_id($analysis_id);
@@ -140,11 +140,11 @@ sub register_worker_death {
   $sth->finish;
 
   if($worker->cause_of_death eq "NO_WORK") {
-    $self->db->get_AnalysisStatsAdaptor->update_status($worker->analysis->dbID, "ALL_CLAIMED");
+    $self->_analysisStatsAdaptor->update_status($worker->analysis->dbID, "ALL_CLAIMED");
   }
   if($worker->cause_of_death eq "FATALITY") {
     #print("FATAL DEATH Arrrrgggghhhhhhhh (hive_id=",$worker->hive_id,")\n");
-    $self->db->get_AnalysisJobAdaptor->reset_dead_jobs_for_worker($worker);
+    $self->_analysisJobAdaptor->reset_dead_jobs_for_worker($worker);
   }
 }
 
@@ -181,14 +181,14 @@ sub update_analysis_stats {
             "WHERE analysis_job.analysis_id=analysis.analysis_id ".
             "GROUP BY analysis_job.analysis_id, status";
 
-  my $statsDBA = $self->db->get_AnalysisStatsAdaptor;
+  my $statsDBA = $self->_analysisStatsAdaptor;
   my $analysisStats = undef;
 
   my $sth = $self->prepare($sql);
   $sth->execute();
   while (my ($analysis_id, $status, $count)=$sth->fetchrow_array()) {
     unless(defined($analysisStats) and $analysisStats->analysis_id==$analysis_id) {
-      $analysisStats->determine_status->update() if($analysisStats);
+      $analysisStats->determine_status()->update() if($analysisStats);
 
       $analysisStats = $statsDBA->fetch_by_analysis_id($analysis_id);
       $analysisStats->total_job_count(0);
@@ -211,23 +211,102 @@ sub update_analysis_stats {
     }
     if($status eq 'DONE') { $analysisStats->done_job_count($count); }
   }
-  $analysisStats->determine_status->update() if($analysisStats);
+  $analysisStats->determine_status()->update() if($analysisStats);
+  $sth->finish;
+
+  $self->adjust_stats_for_living_workers();
+}
+
+
+sub adjust_stats_for_living_workers {
+  my $self = shift;
+
+  my $statsDBA = $self->_analysisStatsAdaptor;
+  
+  my $sql = "SELECT analysis_id, count(*) FROM hive ".
+            "WHERE cause_of_death='' GROUP BY analysis_id";
+  my $sth = $self->prepare($sql);
+  $sth->execute();
+  while (my ($analysis_id, $liveCount)=$sth->fetchrow_array()) {
 
+    my $analysis_stats = $statsDBA->fetch_by_analysis_id($analysis_id);
+
+    if($analysis_stats->hive_capacity > 0) {
+      my $numWorkers = $analysis_stats->num_required_workers;
+
+      my $capacityAdjust = ($numWorkers + $liveCount) - $analysis_stats->hive_capacity;
+      $numWorkers -= $capacityAdjust if($capacityAdjust > 0);
+      $numWorkers=0 if($numWorkers<0);
+
+      $analysis_stats->num_required_workers($numWorkers);
+      $analysis_stats->update;
+    }
+  }
   $sth->finish;
 }
 
 
+sub next_clutch {
+  my $self = shift;
+
+  my $clutches = $self->_analysisStatsAdaptor->fetch_by_needed_workers();
+  return (0, 0) unless($clutches);
+
+  my $smallestClutch = undef;
+  
+  # keep simple : return the clutch with the smallest number of workers first
+  #print("\nCheck for CLUTCH!!\n");
+  foreach my $analysis_stats (@{$clutches}) {
+    #$analysis_stats->print_stats();
+
+    $smallestClutch = $analysis_stats unless($smallestClutch);
+    if($analysis_stats->num_required_workers < $smallestClutch->num_required_workers) {
+      $smallestClutch = $analysis_stats;
+    }
+  }
+  
+  if($smallestClutch) {
+    return ($smallestClutch->analysis_id, $smallestClutch->num_required_workers);
+  }
+  return (0,0);
+}
+
+
 
 #
 # INTERNAL METHODS
 #
 ###################
 
+sub _analysisStatsAdaptor {
+  my $self = shift;
+  unless($self->{'analysisStatsDBA'}) {
+    $self->{'analysisStatsDBA'} = new Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor($self->db);
+  }
+  return $self->{'analysisStatsDBA'};
+}
+
+sub _analysisJobAdaptor {
+  my $self = shift;
+  unless($self->{'analysisJobDBA'}) {
+    $self->{'analysisJobDBA'} = new Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor($self->db);
+  }
+  return $self->{'analysisJobDBA'};
+}
+
+sub _analysisAdaptor {
+  my $self = shift;
+  unless($self->{'analysisDBA'}) {
+    $self->{'analysisDBA'} = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor($self->db);
+  }
+  return $self->{'analysisDBA'};
+}
+
 =head2 _fetch_by_hive_id
 
   Arg [1]    : int $id
                the unique database identifier for the feature to be obtained
-  Example    : $feat = $adaptor->fetch_by_dbID(1234);
+  Example    : $feat = $queen->fetch_by_dbID(1234);
   Description: Returns the feature created from the database defined by the
                the id $id.
   Returntype : Bio::EnsEMBL::Hive::Worker
@@ -361,11 +440,11 @@ sub _objs_from_sth {
     $worker->last_check_in($column{'last_check_in'});
     $worker->died($column{'died'});
     $worker->cause_of_death($column{'cause_of_death'});
-    $worker->adaptor($self);
+    $worker->queen($self);
     $worker->db($self->db);
 
-    if($column{'analysis_id'} and $self->db->get_AnalysisAdaptor) {
-      $worker->analysis($self->db->get_AnalysisAdaptor->fetch_by_dbID($column{'analysis_id'}));
+    if($column{'analysis_id'} and $self->_analysisAdaptor) {
+      $worker->analysis($self->_analysisAdaptor->fetch_by_dbID($column{'analysis_id'}));
     }
 
     push @workers, $worker;