Bio::GMOD::Admin::Monitor::blat - Monitor a BLAT server

Bio-GMOD documentation Contained in the Bio-GMOD distribution.

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NAME

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Bio::GMOD::Admin::Monitor::blat - Monitor a BLAT server

SYNOPSIS

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Check the installed version of a MOD

  use Bio::GMOD::Util::CheckVersions.pm
  my $gmod    = Bio::GMOD::Util::CheckVersions->new(-mod=>'WormBase');
  my $version = $gmod->live_version;

Update a MOD installation

  use Bio::GMOD::Update;
  my $gmod = Bio::GMOD::Update->new(-mod=>'WormBase');
  $gmod->update();

Build archives of MOD releases (coming soon...)

Do some common datamining tasks (coming soon...)

DESCRIPTION

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Bio::GMOD is a unified API for accessing various Model Organism Databases. It is a part of the Generic Model Organism Database project, as well as distributed on CPAN.

MODs are highly curated resources of biological knowledge. MODs typically incorporate the typical information found at common community sites such as NCBI. However, they greatly extend this information, placing it within a framework of experimental and published observations of biological function gleaned from experiments in model organisms.

Given the great proliferation of MODs, cross-site data mining strategies have been difficult to implement. Furthermore, the quickly-evolving nature of these projects have made installing a MOD locally and keeping it up-to-date a delicate and time-consuming experience.

Bio::GMOD aims to solve these problems by:

   1.  Making MODs easy to install
   2.  Making MODs easy to upgrade
   3.  Enabling cross-MOD data mining through a unified API
   4.  Insulating programmatic end users from model changes

NOTES FOR DEVELOPERS

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Bio::GMOD.pm uses a generically subclass-able architecture that lets MOD developers support various features as needed or desired. For example, a developer may wish to override the default methods for Update.pm by building a Bio::GMOD::Update::FlyBase package that provides an update() method, as well as various supporting methods.

Currently, the only participating MOD is WormBase. The authors hope that this will change in the future!

PUBLIC METHODS

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Bio-GMOD documentation Contained in the Bio-GMOD distribution. 
package Bio::GMOD::Admin::Monitor::blat;

# Monitor and restart blat as necessary

use strict;
use vars qw/@ISA/;
use Bio::GMOD::Admin::Monitor;
use Bio::GMOD::Util::Rearrange;
use DBI;

@ISA = qw/Bio::GMOD::Admin::Monitor/;


use strict;

use constant BLAT_SERVER      => '/usr/local/blat/bin/gfServer';
use constant DAEMON_PATH      => '/etc/rc.d/init.d/blat_server';
use constant ALTERNATIVE_PATH => '/usr/local/wormbase/util/admin/blat_server.initd';

my $result = `/usr/local/blat/bin/gfClient localhost 2003 /usr/local/wormbase/blat stdin stdout -nohead < /usr/local/wormbase/blat/test.fa`;
unless ($result) { # can't connect
  warn scalar(localtime),": can't connect to blat server, restarting\n";
  my $result;
  if (-e DAEMON_PATH) {
    $result = system (DAEMON_PATH,'condrestart');
  } else {
    $result = system(ALTERNATIVE_PATH);
  }
  ($result ==0 ) or warn "Restarting the blat server failed: $!\n";
}



/usr/local/blat/bin/gfServer start localhost 2003 /usr/local/wormbase/blat/*.nib & > /dev/null 2>&1
/usr/local/blat/bin/gfServer start localhost 2004 /usr/local/wormbase/blat/briggsae/files/*.nib & > /dev/null 2>&1




sub new {
  my $class = shift;
  my $this   = bless {},$class;
  return $this;
}

sub check_status {
  my ($self,@p) = @_;
  my ($testdb) = rearrange([qw/TESTDB/],@p);
  $testdb ||= 'test';

  $self->{testing}   = 'mysqld';
  $self->{tested_at} = $self->fetch_date;

  my $db = DBI->connect("dbi:mysql:$testdb",'nobody');

  # Populate some redundant tags
  if ($db) {
    $self->set_status_flags('initial','up');
    $self->status_string(-timing => 'initial',
			 -msg    => 'Testing mysqld',
			 -status => 'UP');
  } else {
    $self->set_status_flags('initial','down');
    $self->status_string(-timing => 'initial',
			 -msg    => 'Testing mysqld',
			 -status => 'DOWN');
  }
}



sub restart {
  my ($self,@p) = @_;
  my ($mysqld,$initd,$testdb) = rearrange([qw/MYSQLD INITD TESTDB/],@p);
  if (-e $mysqld) {
    system("$mysqld --user=mysql &")
  } elsif (-e $initd) {
    system("$initd condrestart");
  } else {}

  $testdb ||= 'test';
  my $db = DBI->connect("dbi:mysql:$testdb",'nobody');

  if ($db) {
    $self->set_status_flags('final','up');
    $self->status_string(-timing => 'final',
			 -msg    => "Restarting mysqld via $initd",
			 -status => 'SUCCEEDED');
  } else {
    $self->set_status_flags('final','down');
    $self->status_string(-timing => 'final',
			 -msg    => "Restarting mysqld via $mysqld",
			 -status => 'FAILED');
  }
}





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