pass in a Valley instead of the current_meadow (preparatory)

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -286,11 +286,13 @@ sub register_worker_death {
 }
 
 sub check_for_dead_workers {    # a bit counter-intuitively only looks for current meadow's workers, not all of the dead workers.
-    my ($self, $meadow, $check_buried_in_haste) = @_;
+    my ($self, $valley, $check_buried_in_haste) = @_;
 
-    my $worker_status_hash    = $meadow->status_of_all_our_workers();
-    my %worker_status_summary = ();
-    my $queen_worker_list     = $self->fetch_overdue_workers(0);    # maybe it should return a {meadow->worker_count} hash instead?
+    my $meadow                  = $valley->get_current_meadow();
+
+    my $worker_status_hash      = $meadow->status_of_all_our_workers();
+    my %worker_status_summary   = ();
+    my $queen_worker_list       = $self->fetch_overdue_workers(0);    # maybe it should return a {meadow->worker_count} hash instead?
 
     print "====== Live workers according to    Queen:".scalar(@$queen_worker_list).", Meadow:".scalar(keys %$worker_status_hash)."\n";
 
@@ -739,7 +741,9 @@ sub schedule_workers {
 
 
 sub schedule_workers_resync_if_necessary {
-    my ($self, $meadow, $analysis) = @_;
+    my ($self, $valley, $analysis) = @_;
+
+    my $meadow              = $valley->get_current_meadow();
 
     my $pending_by_rc_id    = ($meadow->can('count_pending_workers_by_rc_id') and $meadow->pending_adjust()) ? $meadow->count_pending_workers_by_rc_id() : {};
     my $submit_limit        = $meadow->submit_workers_max();
@@ -754,7 +758,7 @@ sub schedule_workers_resync_if_necessary {
     unless( keys %$workers_to_run_by_rc_id or $self->get_hive_current_load() or $self->count_running_workers() ) {
         print "*** nothing is running and nothing to do (according to analysis_stats) => perform a hard resync\n" ;
 
-        $self->check_for_dead_workers($meadow, 1);
+        $self->check_for_dead_workers($valley, 1);
         $self->synchronize_hive($analysis);
 
         $workers_to_run_by_rc_id = $self->schedule_workers($analysis, $pending_by_rc_id, $available_submit_limit);

scripts/beekeeper.pl

@@ -200,7 +200,7 @@ sub main {
 
     if($remove_analysis_id) { remove_analysis_id($self, $remove_analysis_id); }
     if($all_dead)           { $queen->register_all_workers_dead(); }
-    if($check_for_dead)     { $queen->check_for_dead_workers($current_meadow, 1); }
+    if($check_for_dead)     { $queen->check_for_dead_workers($valley, 1); }
 
     if ($kill_worker_id) {
         my $worker = $queen->fetch_by_dbID($kill_worker_id);
@@ -232,7 +232,7 @@ sub main {
 
     if ($max_loops) { # positive $max_loop means limited, negative means unlimited
 
-        run_autonomously($self, $max_loops, $keep_alive, $queen, $current_meadow, $analysis);
+        run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $analysis);
 
     } else {
             # the output of several methods will look differently depending on $analysis being [un]defined
@@ -344,13 +344,14 @@ sub generate_worker_cmd {
 }
 
 sub run_autonomously {
-    my ($self, $max_loops, $keep_alive, $queen, $current_meadow, $this_analysis) = @_;
+    my ($self, $max_loops, $keep_alive, $queen, $valley, $this_analysis) = @_;
 
     unless(`runWorker.pl`) {
         print("can't find runWorker.pl script.  Please make sure it's in your path\n");
         exit(1);
     }
 
+    my $current_meadow = $valley->get_current_meadow();
     my $worker_cmd = generate_worker_cmd($self);
 
         # pre-hash the resource_class xparams for future use:
@@ -369,7 +370,7 @@ sub run_autonomously {
 
         print("\n======= beekeeper loop ** $iteration **==========\n");
 
-        $queen->check_for_dead_workers($current_meadow, 0);
+        $queen->check_for_dead_workers($valley, 0);
 
         $queen->print_analysis_status unless($self->{'no_analysis_stats'});
         $queen->print_running_worker_status;