turning the max_limbo_seconds into a JSON config parameter that can be as...

turning the max_limbo_seconds into a JSON config parameter that can be as Meadow-specific as you wish

hive_config.json

@@ -8,6 +8,7 @@
     },
     "Meadow" : {
         "CleanupTempDirectoryKilledWorkers" : 0,
+        "MaxLimboSeconds"                   : 10,
         "LOCAL" : {
             "TotalRunningWorkersMax"   : 2,
             "my-quadcore-desktop" : {

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -108,20 +108,6 @@ sub object_class {
 }
 
 
-############################
-#
-# Queen attributes
-#
-############################
-
-
-sub max_limbo_seconds {
-    my $self = shift;
-    $self->{'_max_limbo_seconds'} = shift if(@_);
-    return $self->{'_max_limbo_seconds'};
-}
-
-
 ############################
 #
 # PUBLIC API
@@ -515,9 +501,12 @@ sub check_for_dead_workers {    # scans the whole Valley for lost Workers (but i
                     $self->update( $worker, @updated_attribs ) if(scalar(@updated_attribs));
                 }
 
+                my $max_limbo_seconds = $this_meadow->config_get('MaxLimboSeconds') // 0;   # The maximum time for a Meadow to start showing the Worker (even in PEND state) after submission.
+                                                                                            # We use it as a timeout for burying SUBMITTED and Meadow-invisible entries in the 'worker' table.
+
                 if( ($worker->status eq 'LOST')
                  || $worker->when_died                                                      # reported by Meadow as DEAD (only if Meadow supports get_report_entries_for_process_ids)
-                 || ($worker->seconds_since_when_submitted > $self->max_limbo_seconds) ) {  # SUBMITTED and waited in limbo (not yet registered) for too long => we consider them LOST
+                 || ($worker->seconds_since_when_submitted > $max_limbo_seconds) ) {        # SUBMITTED and Meadow-invisible for too long => we consider them LOST
 
                     $worker->cause_of_death('LIMBO') if( ($worker->status eq 'SUBMITTED') and !$worker->cause_of_death);    # LIMBO cause_of_death means: found in SUBMITTED state, exceeded the timeout, Meadow did not tell us more
 

scripts/beekeeper.pl

@@ -86,7 +86,6 @@ sub main {
     $self->{'submit_log_dir'}       = undef;
     $self->{'worker_delay_startup_seconds'} = undef;
     $self->{'worker_crash_on_startup_prob'} = undef;
-    $self->{'max_limbo_seconds'}    = 30;
 
     # store all the options passed on the command line for registration
     # we re-create this a bit later, so that we can protect any passwords
@@ -134,9 +133,6 @@ sub main {
                'worker_delay_startup_seconds=i' => \$self->{'worker_delay_startup_seconds'},
                'worker_crash_on_startup_prob=f' => \$self->{'worker_crash_on_startup_prob'},
 
-                    # queen attributes:
-               'max_limbo_seconds=i'            => \$self->{'max_limbo_seconds'},
-
                     # other commands/options
                'h|help!'           => \$help,
                'v|version|versions!'    => \$report_versions,
@@ -268,10 +264,6 @@ sub main {
 
     my $queen = $self->{'dba'}->get_Queen;
 
-    foreach my $queen_attrib (qw(max_limbo_seconds)) {
-        $queen->$queen_attrib( $self->{$queen_attrib} ) if defined($self->{$queen_attrib});
-    }
-
     if($reset_job_id) { $queen->reset_job_by_dbID_and_sync($reset_job_id); }
 
     if($job_id_for_output) {
@@ -790,7 +782,6 @@ __DATA__
     -hive_log_dir <path>                    : directory where stdout/stderr of the hive is redirected
     -worker_delay_startup_seconds <number>  : number of seconds each worker has to wait before first talking to the database (0 by default, useful for debugging)
     -worker_crash_on_startup_prob <float>   : probability of each worker failing at startup (0 by default, useful for debugging)
-    -max_limbo_seconds <number>             : timeout for dumb Meadows for burying Workers that stay in SUBMITTED state for too long and are therefore considered LOST
     -debug <debug_level>                    : set debug level of the workers
 
 =head2 Other commands/options