added schema and API support for meadow_name

modules/Bio/EnsEMBL/Hive/Meadow.pm

@@ -59,7 +59,7 @@ sub generate_job_name {
 sub responsible_for_worker {
     my ($self, $worker) = @_;
 
-    return $worker->meadow_type() eq $self->type();
+    return ($worker->meadow_type eq $self->type) && ($worker->meadow_name eq $self->name);
 }
 
 sub check_worker_is_alive_and_mine {

modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm

@@ -14,6 +14,12 @@ sub available {     # always invoked as a class method
 }
 
 
+sub name {
+
+    return hostname();
+}
+
+
 sub total_running_workers_default_max {
 
     return 2;
@@ -26,6 +32,7 @@ sub get_current_worker_process_id {
     return $$;
 }
 
+
 sub count_running_workers {
     my $self = shift @_;
 
@@ -36,11 +43,6 @@ sub count_running_workers {
     return $run_count;
 }
 
-sub responsible_for_worker {
-    my ($self, $worker) = @_;
-
-    return ( $self->SUPER::responsible_for_worker($worker) && ($worker->host eq hostname()) );
-}
 
 sub status_of_all_our_workers { # returns a hashref
     my ($self) = @_;
@@ -76,6 +78,7 @@ sub status_of_all_our_workers { # returns a hashref
     return \%status_hash;
 }
 
+
 sub check_worker_is_alive_and_mine {
     my ($self, $worker) = @_;
 
@@ -86,6 +89,7 @@ sub check_worker_is_alive_and_mine {
     return $is_alive_and_mine;
 }
 
+
 sub kill_worker {
     my ($self, $worker) = @_;
 
@@ -101,6 +105,7 @@ sub kill_worker {
     }
 }
 
+
 sub submit_workers {
     my ($self, $iteration, $worker_cmd, $worker_count, $rc_id, $rc_parameters) = @_;
 

modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm

@@ -12,6 +12,15 @@ sub available {     # always invoked as a class method
     return `which bjobs 2>/dev/null`;
 }
 
+sub name {
+
+    my $mcni = 'My cluster name is';
+    if(my $name = `lsid | grep '$mcni'`) {
+        $name=~/^$mcni\s+(\w+)/;
+        return $1;
+    }
+}
+
 
 sub get_current_worker_process_id {
     my ($self) = @_;

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -97,11 +97,11 @@ use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
 sub create_new_worker {
   my ($self, @args) = @_;
 
-  my (  $meadow_type, $process_id, $exec_host,
+  my (  $meadow_type, $meadow_name, $process_id, $exec_host,
         $rc_id, $logic_name, $analysis_id, $input_id, $job_id,
         $no_write, $debug, $worker_output_dir, $hive_output_dir, $job_limit, $life_span, $no_cleanup, $retry_throwing_jobs) =
 
- rearrange([qw(meadow_type process_id exec_host
+ rearrange([qw(meadow_type meadow_name process_id exec_host
         rc_id logic_name analysis_id input_id job_id
         no_write debug worker_output_dir hive_output_dir job_limit life_span no_cleanup retry_throwing_jobs) ], @args);
 
@@ -198,11 +198,11 @@ sub create_new_worker {
   }
 
   my $sql = q{INSERT INTO worker 
-              (born, last_check_in, meadow_type, process_id, host, analysis_id)
-              VALUES (CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, ?,?,?,?)};
+              (born, last_check_in, meadow_type, meadow_name, process_id, host, analysis_id)
+              VALUES (CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, ?,?,?,?,?)};
 
   my $sth = $self->prepare($sql);
-  $sth->execute($meadow_type, $process_id, $exec_host, $analysisStats->analysis_id);
+  $sth->execute($meadow_type, $meadow_name, $process_id, $exec_host, $analysisStats->analysis_id);
   my $worker_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'worker', 'worker_id');
   $sth->finish;
 
@@ -1016,6 +1016,7 @@ sub _columns {
   return qw (w.worker_id
              w.analysis_id
              w.meadow_type
+             w.meadow_name
              w.host
              w.process_id
              w.work_done
@@ -1041,6 +1042,7 @@ sub _objs_from_sth {
 
     $worker->dbID($column{'worker_id'});
     $worker->meadow_type($column{'meadow_type'});
+    $worker->meadow_name($column{'meadow_name'});
     $worker->host($column{'host'});
     $worker->process_id($column{'process_id'});
     $worker->work_done($column{'work_done'});

modules/Bio/EnsEMBL/Hive/Valley.pm

@@ -97,14 +97,15 @@ sub current_meadow_class {
 }
 
 
-sub guess_current_type_pid_exechost {
+sub whereami {
     my $self = shift @_;
 
-    my ($type, $pid);
+    my ($meadow_type, $meadow_name, $pid);
     foreach my $meadow_class (@{ $self->get_available_meadow_classes_list }) {
         eval {
-            $pid = $meadow_class->get_current_worker_process_id();
-            $type = $meadow_class->type();
+            $pid         = $meadow_class->get_current_worker_process_id();
+            $meadow_type = $meadow_class->type();
+            $meadow_name = $meadow_class->name();
         };
         unless($@) {
             last;
@@ -116,7 +117,7 @@ sub guess_current_type_pid_exechost {
 
     my $exechost = hostname();
 
-    return ($type, $pid, $exechost);
+    return ($meadow_type, $meadow_name, $pid, $exechost);
 }
 
 

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -114,6 +114,11 @@ sub meadow_type {
   $self->{'_meadow_type'} = shift if(@_);
   return $self->{'_meadow_type'};
 }
+sub meadow_name {
+  my $self = shift;
+  $self->{'_meadow_name'} = shift if(@_);
+  return $self->{'_meadow_name'};
+}
 sub debug {
   my $self = shift;
   $self->{'_debug'} = shift if(@_);

scripts/runWorker.pl

@@ -89,9 +89,9 @@ unless($DBA and $DBA->isa("Bio::EnsEMBL::Hive::DBSQL::DBAdaptor")) {
 
 my $queen = $DBA->get_Queen();
 
-my ($meadow_type, $process_id, $exec_host) = Bio::EnsEMBL::Hive::Valley->new()->guess_current_type_pid_exechost();
+my ($meadow_type, $meadow_name, $process_id, $exec_host) = Bio::EnsEMBL::Hive::Valley->new()->whereami();
 
-print "runWorker(-MeadowType => $meadow_type, -ProcessId => $process_id, -ExecHost => $exec_host)\n";
+print "runWorker(-MeadowType => $meadow_type, -MeadowName => $meadow_name, -ProcessId => $process_id, -ExecHost => $exec_host)\n";
 
 my $worker;
 
@@ -99,6 +99,7 @@ eval {
     $worker = $queen->create_new_worker(
       # Worker identity:
          -meadow_type           => $meadow_type,
+         -meadow_name           => $meadow_name,
          -process_id            => $process_id,
          -exec_host             => $exec_host,
 

sql/patch_2012-05-18.sql

+
+-- add a way to distinguish between meadows of the same type:
+ALTER TABLE worker ADD COLUMN meadow_name VARCHAR(40) AFTER meadow_type;

sql/tables.sql

@@ -108,6 +108,7 @@ CREATE TABLE worker (
   worker_id        int(10) unsigned NOT NULL AUTO_INCREMENT,
   analysis_id      int(10) unsigned NOT NULL,
   meadow_type      enum('LSF', 'LOCAL') NOT NULL,
+  meadow_name      varchar(40) DEFAULT NULL,
   host	           varchar(40) DEFAULT NULL,
   process_id       varchar(40) DEFAULT NULL,
   work_done        int(11) DEFAULT '0' NOT NULL,

sql/tables.sqlite

@@ -98,6 +98,7 @@ CREATE TABLE worker (
   worker_id        INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
   analysis_id      INTEGER NOT NULL,
   meadow_type      TEXT NOT NULL, /* enum('LSF', 'LOCAL') NOT NULL, */
+  meadow_name      varchar(40) DEFAULT NULL,
   host	           varchar(40) DEFAULT NULL,
   process_id       varchar(40) DEFAULT NULL,
   work_done        int(11) DEFAULT '0' NOT NULL,