[Gmod-schema-cmts] schema/chado/lib/Bio/GMOD/DB Adapter.pm, 1.63, 1.64

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/lib/Bio/GMOD/DB
In directory ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv29169/lib/Bio/GMOD/DB

Modified Files:
	Adapter.pm 
Log Message:
adding a load lock so that only one bulk load instance can run at a time


Index: Adapter.pm
===================================================================
RCS file: /cvsroot/gmod/schema/chado/lib/Bio/GMOD/DB/Adapter.pm,v
retrieving revision 1.63
retrieving revision 1.64
diff -C2 -d -r1.63 -r1.64
*** Adapter.pm	1 Sep 2009 19:09:36 -0000	1.63
--- Adapter.pm	4 Sep 2009 19:51:44 -0000	1.64
***************
*** 7,10 ****
--- 7,11 ----
  use Data::Dumper;
  use URI::Escape;
+ use Sys::Hostname;
  use Bio::SeqFeature::Generic;
  use Bio::GMOD::DB::Adapter::FeatureIterator;
***************
*** 183,186 ****
--- 184,199 ----
                    VALUES (?,?,?,?)";
  
+ use constant CREATE_META_TABLE =>
+                "CREATE TABLE gff_meta (
+                      name        varchar(100),
+                      hostname    varchar(100),
+                      starttime   timestamp not null default now() 
+                 )";
+ use constant SELECT_FROM_META =>
+                "SELECT name,hostname,starttime FROM gff_meta";
+ use constant INSERT_INTO_META =>
+                "INSERT INTO gff_meta (name,hostname) VALUES (?,?)";
+ use constant DELETE_FROM_META =>
+                "DELETE FROM gff_meta";
  
  my $ALLOWED_UNIQUENAME_CACHE_KEYS =
***************
*** 1196,1199 ****
--- 1209,1317 ----
  }
  
+ =head2 place_lock
+ 
+ =over
+ 
+ =item Usage
+ 
+   $obj->place_lock()
+ 
+ =item Function
+ 
+ To place a row in the gff_meta table (creating that table if necessary) 
+ that will prevent other users/processes from doing GFF bulk loads while
+ the current process is running.
+ 
+ =item Returns
+ 
+ Nothing
+ 
+ =item Arguments
+ 
+ None
+ 
+ =back
+ 
+ =cut
+ 
+ sub place_lock {
+     my ($self, %argv) = @_;
+ 
+     #first determine if the meta table exists
+     my $dbh = $self->dbh;
+     my $sth = $dbh->prepare(VERIFY_TMP_TABLE);
+     $sth->execute('gff_meta');
+ 
+     my ($table_exists) = $sth->fetchrow_array;
+ 
+     if (!$table_exists) {
+        print STDERR "Creating gff_meta table...\n";
+        $dbh->do(CREATE_META_TABLE); 
+     } 
+ 
+     #check for existing lock
+     my $select_query = $dbh->prepare(SELECT_FROM_META);
+     $select_query->execute();
+     my @result = $select_query->fetchrow_array;
+ 
+     if (scalar @result > 0) {
+         my ($name,$host,$time) = @result;
+         my (undef,$pid)  = split /\-/, $name;
+ 
+         print STDERR "\n\n\nWARNING: There is another gmod_bulk_load_gff3.pl process\n";
+         print STDERR "running on $host, with a process id of $pid\n";
+         print STDERR "which started at $time\n";
+         print STDERR "\nIf that process is no longer running, you can remove the lock by providing\n";
+         print STDERR "the --remove_lock flag when running gmod_bulk_load_gff3.pl\n\n";
+         print STDERR "Note that if the last bulk load process crashed, you may also need the\n";
+         print STDERR "--recreate_cache option as well\n\n";
+ 
+         exit(-2);
+     }
+ 
+ 
+     my $pid = $$;
+     my $name = "gmod_bulk_load_gff3.pl-$pid";
+     my $hostname = hostname;
+ 
+     my $insert_query = $dbh->prepare(INSERT_INTO_META);
+     $insert_query->execute($name,$hostname);
+ 
+     return;
+ }
+ 
+ =head2 remove_lock
+ 
+ =over
+ 
+ =item Usage
+ 
+   $obj->remove_lock()
+ 
+ =item Function
+ 
+ To remove the row in the gff_meta table that prevents other gmod_bulk_load_gff3.pl processes from running while the current process is running.
+ 
+ =item Returns
+ 
+ Nothing
+ 
+ =item Arguments
+ 
+ Nothing
+ 
+ =back
+ 
+ =cut
+ 
+ sub remove_lock {
+     my ($self, %argv) = @_;
+ 
+     my $dbh = $self->dbh;
+     $dbh->do(DELETE_FROM_META);
+ 
+     return;
+ }
+ 
  
  =head2 initialize_ontology