remove the per-worker batch_size flag from scripts

scripts/beekeeper.pl

@@ -94,13 +94,14 @@ sub main {
 
                     # worker control
                'job_limit|jlimit=i'     => \$self->{'job_limit'},
-               'batch_size=i'           => \$self->{'batch_size'},
                'life_span|lifespan=i'   => \$self->{'life_span'},
                'logic_name=s'      => \$self->{'logic_name'},
                'hive_output_dir=s' => \$self->{'hive_output_dir'},
                'maximise_concurrency=i' => \$self->{'maximise_concurrency'},
                'retry_throwing_jobs=i'  => \$self->{'retry_throwing_jobs'},
 
+               'batch_size=i'           => \$self->{'batch_size'},      # OBSOLETE!
+
                     # other commands/options
                'h|help'            => \$help,
                'sync'              => \$sync,
@@ -123,6 +124,11 @@ sub main {
 
     if ($help) { script_usage(0); }
 
+    if( $self->{'batch_size'} ) {
+        print "\nERROR : -batch_size flag is obsolete, please modify batch_size of the analysis instead\n";
+        script_usage(1);
+    }
+
     parse_conf($self, $conf_file);
 
     if($run or $self->{'run_job_id'}) {
@@ -333,7 +339,7 @@ sub generate_worker_cmd {
     if ($self->{'run_job_id'}) {
         $worker_cmd .= " -job_id ".$self->{'run_job_id'};
     } else {
-        foreach my $worker_option ('batch_size', 'job_limit', 'life_span', 'logic_name', 'maximize_concurrency', 'retry_throwing_jobs', 'hive_output_dir') {
+        foreach my $worker_option ('job_limit', 'life_span', 'logic_name', 'maximize_concurrency', 'retry_throwing_jobs', 'hive_output_dir') {
             if(defined(my $value = $self->{$worker_option})) {
                 $worker_cmd .= " -${worker_option} $value";
             }
@@ -510,13 +516,14 @@ __DATA__
 =head2 Worker control
 
     -job_limit <num>            : #jobs to run before worker can die naturally
-    -batch_size <num>           : #jobs a worker can claim at once
     -life_span <num>            : life_span limit for each worker
     -logic_name <string>        : restrict the pipeline stat/runs to this analysis logic_name
     -maximise_concurrency 1     : try to run more different analyses at the same time
     -retry_throwing_jobs 0|1    : if a job dies *knowingly*, should we retry it by default?
     -hive_output_dir <path>     : directory where stdout/stderr of the hive is redirected
 
+    -batch_size <num>           : [OBSOLETE!] Please modify batch_size of the analysis instead
+
 =head2 Other commands/options
 
     -help                  : print this help

scripts/runWorker.pl

@@ -45,7 +45,6 @@ GetOptions(
            'job_id=i'                   => \$job_id,
 
 # Worker control parameters:
-           'batch_size=i'               => \$batch_size,
            'job_limit|limit=i'          => \$job_limit,
            'life_span|lifespan=i'       => \$life_span,
            'no_cleanup'                 => \$no_cleanup,
@@ -54,6 +53,8 @@ GetOptions(
            'worker_output_dir=s'        => \$worker_output_dir,     # will take precedence over hive_output_dir if set
            'retry_throwing_jobs=i'      => \$retry_throwing_jobs,
 
+           'batch_size=i'               => \$batch_size,            # OBSOLETE!
+
 # Other commands
            'h|help'                     => \$help,
            'debug=i'                    => \$debug,
@@ -66,6 +67,12 @@ GetOptions(
 
 if ($help) { script_usage(0); }
 
+if( $batch_size ) {
+    print "\nERROR : -batch_size flag is obsolete, please modify batch_size of the analysis instead\n";
+    script_usage(1);
+}
+
+
 parse_conf($conf_file);
 
 if($reg_conf) {     # if reg_conf is defined, we load it regardless of whether it is used to connect to the Hive database or not:
@@ -113,7 +120,6 @@ eval {
          -job_id                => $job_id,
 
       # Worker control parameters:
-         -batch_size            => $batch_size,
          -job_limit             => $job_limit,
          -life_span             => $life_span,
          -no_cleanup            => $no_cleanup,
@@ -122,6 +128,9 @@ eval {
          -hive_output_dir       => $hive_output_dir,
          -retry_throwing_jobs   => $retry_throwing_jobs,
 
+      ## Obsolete:
+      # -batch_size            => $batch_size,
+
       # Other parameters:
          -debug                 => $debug,
     );
@@ -229,7 +238,6 @@ __DATA__
 
 =head2 Worker control parameters:
 
-    -batch_size <num>           : #jobs to claim at a time
     -job_limit <num>            : #jobs to run before worker can die naturally
     -life_span <num>            : number of minutes this worker is allowed to run
     -no_cleanup                 : don't perform temp directory cleanup when worker exits
@@ -238,6 +246,8 @@ __DATA__
     -worker_output_dir <path>   : directory where stdout/stderr of this particular worker is redirected
     -retry_throwing_jobs <0|1>  : if a job dies *knowingly*, should we retry it by default?
 
+    -batch_size <num>           : [OBSOLETE!] Please modify batch_size of the analysis instead
+
 =head2 Other options:
 
     -help                       : print this help