API change: Q::print_analysis_status now takes an obligatory $list_of_analyses

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -700,10 +700,19 @@ sub get_remaining_jobs_show_hive_progress {
 }
 
 
+=head2 print_analysis_status
+
+  Arg [1]    : $list_of_analyses
+  Example    : $queen->print_analysis_status( [ $analysis_A, $analysis_B ] );
+  Description: Runs through all analyses in the given list and prints their stats.
+  Exceptions : none
+  Caller     : beekeeper.pl
+
+=cut
+
 sub print_analysis_status {
-    my ($self, $filter_analysis) = @_;
+    my ($self, $list_of_analyses) = @_;
 
-    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
     foreach my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {
         print $analysis->stats->toString . "\n";
     }
@@ -715,7 +724,7 @@ sub print_analysis_status {
   Example    : $queen->register_all_workers_dead();
   Description: Registers all workers dead
   Exceptions : none
-  Caller     : beekeepers and other external processes
+  Caller     : beekeeper.pl
 
 =cut
 

scripts/beekeeper.pl

@@ -253,7 +253,7 @@ sub main {
 
     if ($max_loops) { # positive $max_loop means limited, negative means unlimited
 
-        run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $analysis, $run_job_id, $force);
+        run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $list_of_analyses, $analysis, $run_job_id, $force);
 
     } else {
             # the output of several methods will look differently depending on $analysis being [un]defined
@@ -261,7 +261,7 @@ sub main {
         if($sync) {
             $queen->synchronize_hive( $list_of_analyses );
         }
-        $queen->print_analysis_status($analysis) unless($self->{'no_analysis_stats'});
+        $queen->print_analysis_status( $list_of_analyses ) unless($self->{'no_analysis_stats'});
 
         if($show_worker_stats) {
             print "\n===== List of live Workers according to the Queen: ======\n";
@@ -326,10 +326,9 @@ sub generate_worker_cmd {
 }
 
 sub run_autonomously {
-    my ($self, $max_loops, $keep_alive, $queen, $valley, $run_analysis, $run_job_id, $force) = @_;
+    my ($self, $max_loops, $keep_alive, $queen, $valley, $list_of_analyses, $run_analysis, $run_job_id, $force) = @_;
 
     my $resourceless_worker_cmd = generate_worker_cmd($self, $run_analysis, $run_job_id, $force);
-    my $special_task            = $run_analysis || $run_job_id;
 
     my $rc_id2name  = $self->{'dba'}->get_ResourceClassAdaptor->fetch_HASHED_FROM_resource_class_id_TO_name();
     my %meadow_type_rc_name2resource_param_list = ();
@@ -353,7 +352,7 @@ sub run_autonomously {
 
         $queen->check_for_dead_workers($valley, 0);
 
-        $queen->print_analysis_status unless($self->{'no_analysis_stats'});
+        $queen->print_analysis_status( $list_of_analyses ) unless($self->{'no_analysis_stats'});
         $self->{'dba'}->get_RoleAdaptor->print_active_role_counts;
 
         my $workers_to_submit_by_meadow_type_rc_name