a more straightforward storing method for an AnalysisJob

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

@@ -100,12 +100,14 @@ sub input_id {
 sub param_id_stack {
     my $self = shift;
     $self->{'_param_id_stack'} = shift if(@_);
+    $self->{'_param_id_stack'} = '' unless(defined($self->{'_param_id_stack'}));
     return $self->{'_param_id_stack'};
 }
 
 sub accu_id_stack {
     my $self = shift;
     $self->{'_accu_id_stack'} = shift if(@_);
+    $self->{'_accu_id_stack'} = '' unless(defined($self->{'_accu_id_stack'}));
     return $self->{'_accu_id_stack'};
 }
 
@@ -118,6 +120,7 @@ sub worker_id {
 sub status {
     my $self = shift;
     $self->{'_status'} = shift if(@_);
+    $self->{'_status'} = ( ($self->semaphore_count>0) ? 'SEMAPHORED' : 'READY' ) unless(defined($self->{'_status'}));
     return $self->{'_status'};
 }
 

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -76,7 +76,7 @@ sub default_overflow_limit {
 
 ###############################################################################
 #
-#  CLASS methods
+#  CLASS method
 #
 ###############################################################################
 
@@ -115,58 +115,64 @@ sub CreateNewJob {
     unless($analysis->adaptor and $analysis->adaptor->db);
   throw("Please specify prev_job object instead of prev_job_id if available") if ($prev_job_id);   # 'obsolete' message
 
-    $prev_job_id        = $prev_job && $prev_job->dbID();
-    $semaphore_count  ||= 0;
-    my $job_status      = ($semaphore_count>0) ? 'SEMAPHORED' : 'READY';
-    my $analysis_id     = $analysis->dbID();
-
     my $job = Bio::EnsEMBL::Hive::AnalysisJob->new(
-        -prev_job_id        => $prev_job_id,
-        -analysis_id        => $analysis_id,
+        -prev_job_id        => $prev_job && $prev_job->dbID,
+        -analysis_id        => $analysis->dbID,
         -input_id           => $input_id,
-        -param_id_stack     => $param_id_stack || '',
-        -accu_id_stack      => $accu_id_stack  || '',
-        -status             => $job_status,
+        -param_id_stack     => $param_id_stack,
+        -accu_id_stack      => $accu_id_stack,
         -semaphore_count    => $semaphore_count,
         -semaphored_job_id  => $semaphored_job_id,
     );
+    
+    return $analysis->adaptor->db->get_AnalysisJobAdaptor->store_job_and_adjust_counters( $job, $push_new_semaphore );
+}
+
+
+###############################################################################
+#
+#  INSTANCE methods
+#
+###############################################################################
 
-    my $dba = $analysis->adaptor->db;
-    my $dbc = $dba->dbc;
-    $dbc->do( "SELECT 1 FROM job WHERE job_id=$semaphored_job_id FOR UPDATE" ) if($semaphored_job_id and ($dbc->driver ne 'sqlite'));
 
-    my ($job, $stored_this_time) = $dba->get_AnalysisJobAdaptor->store( $job, 0 );
+sub store_job_and_adjust_counters {
+    my ($self, $job, $push_new_semaphore) = @_;
+
+    my $semaphored_job_id                   = $job->semaphored_job_id();
+    my $need_to_increase_semaphore_count    = ($semaphored_job_id && !$push_new_semaphore);
+
+    my $dbc = $self->dbc;
+        # avoid deadlocks when dataflowing under transactional mode (used in Ortheus Runnable for example):
+    $dbc->do( "SELECT 1 FROM job WHERE job_id=$semaphored_job_id FOR UPDATE" ) if($need_to_increase_semaphore_count and ($dbc->driver ne 'sqlite'));
+
+    my ($job, $stored_this_time) = $self->store( $job, 0 );
 
     if($stored_this_time) {
-        if($semaphored_job_id and !$push_new_semaphore) {   # if we are not creating a new semaphore (where dependent jobs have already been counted),
-                                                            # but rather propagating an existing one (same or other level), we have to up-adjust the counter
-            $prev_job->adaptor->increase_semaphore_count_for_jobid( $semaphored_job_id );
+        if($need_to_increase_semaphore_count) { # if we are not creating a new semaphore (where dependent jobs have already been counted),
+                                                # but rather propagating an existing one (same or other level), we have to up-adjust the counter
+            $self->increase_semaphore_count_for_jobid( $semaphored_job_id );
         }
 
-        unless($dba->hive_use_triggers()) {
+        unless($self->db->hive_use_triggers()) {
             $dbc->do(qq{
-                UPDATE analysis_stats
-                SET total_job_count=total_job_count+1
-            }
-            .(($job_status eq 'READY')
-                ? " ,ready_job_count=ready_job_count+1 "
-                : " ,semaphored_job_count=semaphored_job_count+1 "
-            ).(($dbc->driver eq 'pgsql')
-                ? " ,status = CAST(CASE WHEN status!='BLOCKED' THEN 'LOADING' ELSE 'BLOCKED' END AS analysis_status) "
-                : " ,status =      CASE WHEN status!='BLOCKED' THEN 'LOADING' ELSE 'BLOCKED' END "
-            )." WHERE analysis_id=$analysis_id ");
+                    UPDATE analysis_stats
+                    SET total_job_count=total_job_count+1
+                }
+                .(($job->status eq 'READY')
+                    ? " ,ready_job_count=ready_job_count+1 "
+                    : " ,semaphored_job_count=semaphored_job_count+1 "
+                ).(($dbc->driver eq 'pgsql')
+                    ? " ,status = CAST(CASE WHEN status!='BLOCKED' THEN 'LOADING' ELSE 'BLOCKED' END AS analysis_status) "
+                    : " ,status =      CASE WHEN status!='BLOCKED' THEN 'LOADING' ELSE 'BLOCKED' END "
+                )." WHERE analysis_id=".$job->analysis_id
+            );
         }
 
         return $job->dbID();
     }
 }
 
-###############################################################################
-#
-#  INSTANCE methods
-#
-###############################################################################
-
 
 =head2 fetch_all_by_analysis_id_status