moved special-job-reset and special-job-reclaim into the same call, removed...

moved special-job-reset and special-job-reclaim into the same call, removed the unnecessary fetch in between

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

@@ -501,12 +501,12 @@ sub grab_jobs_for_worker {
   my $any_selection_sql     = $selection_start_sql . " LIMIT $how_many_this_batch";
 
   if($self->dbc->driver eq 'sqlite') {
-            # we have to be explicitly numereic here because of '0E0' value returned by DBI if "no rows have been affected":
+            # we have to be explicitly numeric here because of '0E0' value returned by DBI if "no rows have been affected":
       if( (my $claim_count = $self->dbc->do( $update_sql . " WHERE job_id IN (SELECT job_id FROM job $virgin_selection_sql) AND status='READY'" )) == 0 ) {
             $claim_count = $self->dbc->do( $update_sql . " WHERE job_id IN (SELECT job_id FROM job $any_selection_sql) AND status='READY'" );
       }
   } else {
-            # we have to be explicitly numereic here because of '0E0' value returned by DBI if "no rows have been affected":
+            # we have to be explicitly numeric here because of '0E0' value returned by DBI if "no rows have been affected":
       if( (my $claim_count = $self->dbc->do( $update_sql . $virgin_selection_sql )) == 0 ) {
             $claim_count = $self->dbc->do( $update_sql . $any_selection_sql );
       }
@@ -517,11 +517,35 @@ sub grab_jobs_for_worker {
 }
 
 
-sub reclaim_job_for_worker {
-    my ($self, $worker, $job) = @_;
+=head2 reset_job_by_dbID
 
-    my $worker_id   = $worker->dbID();
-    my $job_id      = $job->dbID;
+  Arg [1]    : int $job_id
+  Example    :
+  Description: Forces a job to be reset to 'READY' so it can be run again.
+               FIXME: Will also reset a previously 'SEMAPHORED' jobs to READY.
+               The retry_count will be set to 1 for previously run jobs (partially or wholly) to trigger PRE_CLEANUP for them,
+               but will not change retry_count if a job has never *really* started.
+  Exceptions : $job_id must not be false or zero
+  Caller     : user process
+
+=cut
+
+sub reset_job_by_dbID {
+    my $self        = shift;
+    my $job_id      = shift;
+
+        # Note: the order of the fields being updated is critical!
+    $self->dbc->do( qq{
+        UPDATE job
+           SET retry_count = (CASE WHEN (status='COMPILATION' OR status='READY' OR status='CLAIMED') THEN retry_count ELSE 1 END)
+             , status='READY'
+         WHERE job_id=$job_id
+    } );
+}
+
+
+sub reclaim_job_for_worker {
+    my ($self, $job_id, $worker_id) = @_;
 
     my $sql = "UPDATE job SET status='CLAIMED', worker_id=? WHERE job_id=? AND status='READY'";
 
@@ -652,33 +676,6 @@ sub gc_dataflow {
 }
 
 
-=head2 reset_job_by_dbID
-
-  Arg [1]    : int $job_id
-  Example    :
-  Description: Forces a job to be reset to 'READY' so it can be run again.
-               Will also reset a previously 'SEMAPHORED' jobs to READY (FIXME?).
-               The retry_count will be set to 1 for previously run jobs (partially or wholly) to trigger PRE_CLEANUP for them,
-               but will not change retry_count if a job has never *really* started.
-  Exceptions : $job_id must not be false or zero
-  Caller     : user process
-
-=cut
-
-sub reset_job_by_dbID {
-    my $self   = shift;
-    my $job_id = shift or throw("job_id of the job to be reset is undefined");
-
-        # Note: the order of the fields being updated is critical!
-    $self->dbc->do( qq{
-        UPDATE job
-           SET retry_count = (CASE WHEN (status='COMPILATION' OR status='READY' OR status='CLAIMED') THEN retry_count ELSE 1 END)
-             , status='READY'
-         WHERE job_id=$job_id
-    } );
-}
-
-
 =head2 reset_jobs_for_analysis_id
 
   Arg [1]    : int $analysis_id

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -171,8 +171,7 @@ sub create_new_worker {
 
   Description: If analysis_id or logic_name is specified it will try to specialize the Worker into this analysis.
                If not specified the Queen will analyze the hive and pick the most suitable analysis.
-  Returntype : Bio::EnsEMBL::Hive::Worker
-  Caller     : runWorker.pl
+  Caller     : Bio::EnsEMBL::Hive::Worker
 
 =cut
 
@@ -186,7 +185,7 @@ sub specialize_new_worker {
         die "At most one of the options {-analysis_id, -logic_name, -job_id} can be set to pre-specialize a Worker";
     }
 
-    my ($job, $analysis, $stats);
+    my ($analysis, $stats, $special_batch);
     my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;
 
     if($job_id or $analysis_id or $logic_name) {    # probably pre-specialized from command-line
@@ -197,10 +196,14 @@ sub specialize_new_worker {
             my $job_adaptor = $self->db->get_AnalysisJobAdaptor;
             $job_adaptor->reset_job_by_dbID($job_id); 
 
-            $job = $job_adaptor->fetch_by_dbID($job_id)
-                or die "job with dbID='$job_id' could not be fetched from the database";
+            my $worker_id = $worker->dbID;
+            $special_batch = $job_adaptor->reclaim_job_for_worker($job_id, $worker_id);
 
-            $analysis_id = $job->analysis_id;
+            if(my $job = $special_batch->[0]) {
+                $analysis_id = $job->analysis_id;
+            } else {
+                die "Could not reclaim job with dbID='$job_id' for worker with dbID='$worker_id'";
+            }
         }
 
         if($logic_name) {
@@ -222,7 +225,7 @@ sub specialize_new_worker {
         $stats = $analysis_stats_adaptor->fetch_by_analysis_id($analysis_id);
         $self->safe_synchronize_AnalysisStats($stats);
 
-        unless($job or $force) {    # do we really need to run this analysis?
+        unless($special_batch or $force) {    # do we really need to run this analysis?
             if($self->get_hive_current_load() >= 1.1) {
                 die "Hive is overloaded, can't specialize a worker";
             }
@@ -255,8 +258,8 @@ sub specialize_new_worker {
     $sth_update_analysis_id->execute($worker->analysis_id, $worker->dbID);
     $sth_update_analysis_id->finish;
 
-    if($job) {
-        $worker->_specific_job($job);
+    if($special_batch) {
+        $worker->special_batch( $special_batch );
     } else {    # count it as autonomous worker sharing the load of that analysis:
 
         $stats->update_status('WORKING');
@@ -273,8 +276,6 @@ sub specialize_new_worker {
     unless( $self->db->hive_use_triggers() ) {
         $analysis_stats_adaptor->increase_running_workers($worker->analysis_id);
     }
-
-    return $worker;
 }
 
 

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -245,6 +245,12 @@ sub execute_writes {
 }
 
 
+sub special_batch {
+  my $self = shift;
+  $self->{'_special_batch'} = shift if(@_);
+  return $self->{'_special_batch'};
+}
+
 =head2 analysis
 
   Arg [1] : (optional) Bio::EnsEMBL::Hive::Analysis $value
@@ -534,8 +540,8 @@ sub run {
     my $jobs_done_by_batches_loop   = 0; # by all iterations of internal loop
     $self->{'_interval_partial_timing'} = {};
 
-    if( my $specific_job = $self->_specific_job() ) {
-        $jobs_done_by_batches_loop += $self->run_one_batch( $job_adaptor->reclaim_job_for_worker($self, $specific_job) );
+    if( my $special_batch = $self->special_batch() ) {
+        $jobs_done_by_batches_loop += $self->run_one_batch( $special_batch );
         $self->cause_of_death('JOB_LIMIT'); 
     } else {    # a proper "BATCHES" loop
 
@@ -779,11 +785,4 @@ sub stop_job_output_redirection {
 }
 
 
-sub _specific_job {
-  my $self = shift;
-  $self->{'_specific_job'} = shift if(@_);
-  return $self->{'_specific_job'};
-}
-
-
 1;