API change: synchronize_hive now takes an obligatory $list_of_analyses

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -528,24 +528,21 @@ sub fetch_overdue_workers {
 
 =head2 synchronize_hive
 
-  Arg [1]    : $filter_analysis (optional)
-  Example    : $queen->synchronize_hive();
-  Description: Runs through all analyses in the system and synchronizes
-              the analysis_stats summary with the states in the job 
-              and worker tables.  Then follows by checking all the blocking rules
-              and blocks/unblocks analyses as needed.
+  Arg [1]    : $list_of_analyses
+  Example    : $queen->synchronize_hive( [ $analysis_A, $analysis_B ] );
+  Description: Runs through all analyses in the given list and synchronizes
+              the analysis_stats summary with the states in the job and worker tables.
+              Then follows by checking all the blocking rules and blocks/unblocks analyses as needed.
   Exceptions : none
   Caller     : general
 
 =cut
 
 sub synchronize_hive {
-    my ($self, $filter_analysis) = @_;
+    my ($self, $list_of_analyses) = @_;
 
     my $start_time = time();
 
-    my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;
-
     print STDERR "\nSynchronizing the hive (".scalar(@$list_of_analyses)." analyses this time):\n";
     foreach my $analysis (@$list_of_analyses) {
         $self->synchronize_AnalysisStats($analysis->stats);

modules/Bio/EnsEMBL/Hive/Scheduler.pm

@@ -47,6 +47,9 @@ use Bio::EnsEMBL::Hive::Limiter;
 sub schedule_workers_resync_if_necessary {
     my ($queen, $valley, $filter_analysis) = @_;
 
+    my $list_of_analyses                        = $filter_analysis ? [ $filter_analysis ] : $queen->db->get_AnalysisAdaptor->fetch_all();
+        # $queen->db->get_AnalysisAdaptor->fetch_by_logic_name( $analyses_pattern )
+
     my $submit_capacity                         = $valley->config_get('SubmitWorkersMax');
     my $default_meadow_type                     = $valley->get_default_meadow()->type;
     my $meadow_capacity_limiter_hashed_by_type  = $valley->get_meadow_capacity_hash_by_meadow_type();
@@ -69,15 +72,15 @@ sub schedule_workers_resync_if_necessary {
             $queen->check_for_dead_workers($valley, 1);
         }
 
-        print "Scheduler: re-synchronizing the Hive...\n";
-        $queen->synchronize_hive($filter_analysis);
+        print "Scheduler: re-synchronizing...\n";
+        $queen->synchronize_hive( $list_of_analyses );
 
         if( $queen->db->hive_auto_rebalance_semaphores ) {  # make sure rebalancing only ever happens for the pipelines that asked for it
             if( $queen->check_nothing_to_run_but_semaphored ) { # and double-check on our side
                 print "Scheduler: looks like we may need re-balancing semaphore_counts...\n";
-                if( my $rebalanced_jobs_counter = $queen->db->get_AnalysisJobAdaptor->balance_semaphores($filter_analysis && [ $filter_analysis ] ) ) {
-                    print "Scheduler: re-balanced $rebalanced_jobs_counter jobs, going through another re-synchronization of the Hive...\n";
-                    $queen->synchronize_hive($filter_analysis);
+                if( my $rebalanced_jobs_counter = $queen->db->get_AnalysisJobAdaptor->balance_semaphores( $list_of_analyses ) ) {
+                    print "Scheduler: re-balanced $rebalanced_jobs_counter jobs, going through another re-synchronization...\n";
+                    $queen->synchronize_hive( $list_of_analyses );
                 } else {
                     print "Scheduler: hmmm... managed to re-balance 0 jobs, you may need to investigate further.\n";
                 }

scripts/beekeeper.pl

@@ -242,12 +242,14 @@ sub main {
     }
 
     my $analysis = $run_job_id
-        ? $self->{'dba'}->get_AnalysisAdaptor->fetch_by_dbID( $self->{'dba'}->get_AnalysisJobAdaptor->fetch_by_dbID( $run_job_id )->analysis_id )
+        ? $self->{'dba'}->get_AnalysisJobAdaptor->fetch_by_dbID( $run_job_id )->analysis
         : ( $self->{'logic_name'} && $self->{'dba'}->get_AnalysisAdaptor->fetch_by_logic_name($self->{'logic_name'}) );
 
+    my $list_of_analyses = $analysis ? [ $analysis ] : $self->{'dba'}->get_AnalysisAdaptor->fetch_all();
+
     if($all_dead)           { $queen->register_all_workers_dead(); }
     if($check_for_dead)     { $queen->check_for_dead_workers($valley, 1); }
-    if($balance_semaphores) { $self->{'dba'}->get_AnalysisJobAdaptor->balance_semaphores( $analysis && [ $analysis ] ); }
+    if($balance_semaphores) { $self->{'dba'}->get_AnalysisJobAdaptor->balance_semaphores( $list_of_analyses ); }
 
     if ($max_loops) { # positive $max_loop means limited, negative means unlimited
 
@@ -257,7 +259,7 @@ sub main {
             # the output of several methods will look differently depending on $analysis being [un]defined
 
         if($sync) {
-            $queen->synchronize_hive($analysis);
+            $queen->synchronize_hive( $list_of_analyses );
         }
         $queen->print_analysis_status($analysis) unless($self->{'no_analysis_stats'});