added a new protected_prepare_execute() method to avoid deadlocks and used it...

added a new protected_prepare_execute() method to avoid deadlocks and used it twice in AnalysisJobAdaptor, to fix Stephen's deadlocks

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

@@ -396,9 +396,8 @@ sub increase_semaphore_count_for_jobid {    # used in semaphore propagation
         WHERE job_id=? AND status='SEMAPHORED'
     };
     
-    my $sth = $self->prepare($sql);
-    $sth->execute($inc, $jobid);
-    $sth->finish;
+        # This particular query is infamous for collisions and 'deadlock' situations; let's wait and retry:
+    $self->dbc->protected_prepare_execute( $sql, $inc, $jobid );
 }
 
 
@@ -429,23 +428,8 @@ sub update_status {
 
     $sql .= " WHERE job_id='".$job->dbID."' ";
 
-        # This particular query is infamous for collisions and 'deadlock' situations; let's make them wait and retry.
-    foreach (0..3) {
-        eval {
-            my $sth = $self->prepare($sql);
-            $sth->execute();
-            $sth->finish;
-            1;
-        } or do {
-            if($@ =~ /Deadlock found when trying to get lock; try restarting transaction/) {    # ignore this particular error
-                sleep 1;
-                next;
-            }
-            die $@;     # but definitely report other errors
-        };
-        last;
-    }
-    die "After 3 retries still in a deadlock: $@" if($@);
+        # This particular query is infamous for collisions and 'deadlock' situations; let's wait and retry:
+    $self->dbc->protected_prepare_execute( $sql );
 }
 
 

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

@@ -71,5 +71,29 @@ sub url {
 }
 
 
+sub protected_prepare_execute {     # try to resolve certain mysql "Deadlocks" by trying again (a useful workaround even in mysql 5.1.61)
+    my $self        = shift @_;
+    my $sql         = shift @_;
+
+    my $retries     = 3;
+
+    foreach (0..$retries) {
+        eval {
+            my $sth = $self->prepare($sql);
+            $sth->execute( @_ );
+            $sth->finish;
+            1;
+        } or do {
+            if($@ =~ /Deadlock found when trying to get lock; try restarting transaction/) {    # ignore this particular error
+                sleep 1;
+                next;
+            }
+            die $@;     # but definitely report other errors
+        };
+        last;
+    }
+    die "After $retries retries still in a deadlock: $@" if($@);
+}
+
 1;