renamed for clarity

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

@@ -139,12 +139,12 @@ sub stderr_file {
   return $self->{'_stderr_file'};
 }
 
-sub lethal {    # Job should set this to 1 prior to dying (or before running code that might cause death - such as RunnableDB's compilation)
-                # if it believes that the state of things will not allow the Worker to continue normally.
-                # The Worker will check the flag and commit suicide if it is set to true.
+sub lethal_for_worker {     # Job should set this to 1 prior to dying (or before running code that might cause death - such as RunnableDB's compilation)
+                            # if it believes that the state of things will not allow the Worker to continue normally.
+                            # The Worker will check the flag and commit suicide if it is set to true.
   my $self = shift;
-  $self->{'_lethal'} = shift if(@_);
-  return $self->{'_lethal'};
+  $self->{'_lethal_for_worker'} = shift if(@_);
+  return $self->{'_lethal_for_worker'};
 }
 
 sub print_job {

modules/Bio/EnsEMBL/Hive/RunnableDB/FailureTest.pm

@@ -124,7 +124,7 @@ sub dangerous_math {
 
     if($value % $divisor == 0) {
         if($value>10) { # take the Worker with us into the grave
-            $self->input_job->lethal(1);
+            $self->input_job->lethal_for_worker(1);
         }
 
         die "Preprogrammed death since $value is a multiple of $divisor";

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -517,7 +517,7 @@ sub run
             $self->db()->get_JobErrorAdaptor()->register_error($job_id, $error_msg);
             $job->update_status('FAILED');
 
-            if($job->lethal) {    # either a compilation error or other job-sanctioned contamination
+            if($job->lethal_for_worker) {    # either a compilation error or other job-sanctioned contamination
                 warn "Job's error has contaminated the Worker, so the Worker will now die\n";
                 $self->cause_of_death('CONTAMINATED');
                 last BATCHES;
@@ -593,9 +593,9 @@ sub run_module_with_job {
 
   $self->enter_status('COMPILATION');
   $job->update_status('COMPILATION');
-  $job->lethal(1);  # if it dies in this state, it will kill the Worker
+  $job->lethal_for_worker(1);  # if it dies in this state, it will kill the Worker
   my $runObj = $self->analysis->process or die "Unknown compilation error";
-  $job->lethal(0);  # not dangerous anymore
+  $job->lethal_for_worker(0);  # not dangerous anymore
 
   my $native_hive_process = $runObj->isa("Bio::EnsEMBL::Hive::Process");
   

sql/patch_2010-08-11.sql

@@ -6,7 +6,7 @@ CREATE TABLE job_error (
   worker_id                 int(10) NOT NULL,
   died                      timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
   retry_count               int(10) DEFAULT 0 NOT NULL,
-  status                    enum('COMPILATION','GET_INPUT','RUN','WRITE_OUTPUT'),
+  status                    enum('UNKNOWN','COMPILATION','GET_INPUT','RUN','WRITE_OUTPUT') DEFAULT 'UNKNOWN',
   error_msg                 text,
 
   PRIMARY KEY               (analysis_job_id, worker_id, died),

sql/tables.sql

@@ -166,7 +166,7 @@ CREATE TABLE job_error (
   worker_id                 int(10) NOT NULL,
   died                      timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
   retry_count               int(10) DEFAULT 0 NOT NULL,
-  status                    enum('COMPILATION','GET_INPUT','RUN','WRITE_OUTPUT'),
+  status                    enum('UNKNOWN', 'COMPILATION', 'GET_INPUT', 'RUN', 'WRITE_OUTPUT') DEFAULT 'UNKNOWN',
   error_msg                 text,
 
   PRIMARY KEY               (analysis_job_id, worker_id, died),