Bio-GMOD

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GMOD/Adaptor.pm  view on Meta::CPAN

  my ($self,$overrides) = @_;
  my $adaptor = bless {},$self;
  eval {"require $self"} or $self->logit(-msg => "Couldn't require the $self package: $!",-die => 1);

  # Is a defaults script available?
  # This should be converted to XML
  if ($adaptor->defaults_cgi) {
    my $ua      = LWP::UserAgent->new();
    my $version = $self->biogmod_version;
    $ua->agent("Bio::GMOD.pm/$version");
    my $request = HTTP::Request->new('GET',$adaptor->defaults_cgi);
    my $response = $ua->request($request);

    if ($response->is_success) {
      # Parse out the content and store the defaults in the object
      my $content = $response->content;
      my @lines = split("\n",$content);
      foreach (@lines) {
	next if /^\#/;  # ignore comments
	my ($key,$val) = split("=");
	$adaptor->{defaults}->{lc($key)} = $val;

GMOD/Admin/Monitor/httpd.pm  view on Meta::CPAN

  unless ($site) {
    my $adaptor = $self->adaptor;
    $site = $adaptor->live_url;
  }

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

  my $ua     = LWP::UserAgent->new();
  $ua->agent('Bio::GMOD::Admin::Monitor');
  my $request = HTTP::Request->new('GET',$site);
  my $response = $ua->request($request);
  my ($string,$status) = $self->set_status(-timing => 'initial',
					   -msg    => "Testing httpd at $site",
					   -status => ($response->is_success) ? 'up' : 'down');
  return ($string,$status);
}


# NOTE!  The "final" status is really just whether or not the command
# succeeded, not whether the service has been restored!

GMOD/Query/FlyBase.pm  view on Meta::CPAN

sub protein {  }

sub _do_request {
  my ($self,$params) = @_;
  my $adaptor = $self->adaptor;
  my $url = $adaptor->datamining_url;

  # Create a request
  my $ua = LWP::UserAgent->new();
  my $req = HTTP::Request->new(POST => $url);
  my $version = $self->biogmod_version;
  $ua->agent("Bio::GMOD::Query::FlyBase/$version");

  $req->content_type('application/x-www-form-urlencoded');
  $req->content($params);

  # Pass request to the user agent and get a response back
  my $res = $ua->request($req);

  # Check the outcome of the response

GMOD/StandardURLs.pm  view on Meta::CPAN

  $species = $self->get_shortname($species);
  unless ($url) {
    $release ||= $self->get_current($species);
    $release = $self->get_current($species) if $release eq 'current';
    $self->logit(-msg=>"You must specify a species, dataset, and release") unless ($species && $dataset && $release);
    $url = "$root/genome/$species/$release/$dataset";
  }

  # Does this work?
  my $request = HTTP::Request->new('GET',$url);
  my $response = $ua->request($request);
  $self->logit(-msg=>"Couldn't fetch $url: $!") unless $response->is_success;

  if ($response->is_success) {
    my $content = $response->content();
    return $content;
  }
  return 0;
}

GMOD/StandardURLs.pm  view on Meta::CPAN

}

# Parse the standard URLs XML
sub _parse_xml {
  my $self = shift;
  my $adaptor = $self->adaptor;
  my $standard_urls = $adaptor->standard_urls_xml;
  my $version = $self->biogmod_version;
  my $ua = LWP::UserAgent->new();
  $ua->agent("Bio::GMOD::StandardURLS.pm/$version");
  my $request = HTTP::Request->new('GET',$standard_urls);

  my $response = $ua->request($request);
  die "Couldn't fetch $standard_urls: $!\n" unless $response->is_success;

  my $content = $response->content;
  my $config = XMLin($content);

  # Cache the content for multiple requests
  $self->{standard_urls} = $config;
  return $config;

GMOD/Util/CheckVersions.pm  view on Meta::CPAN

# PRIVATE METHODS
##################################
sub _check_version {
  my ($self,$site,$url) = @_;
  # Version script holds a simple cgi that dumps out the
  # title, release date, and version of the database
  $url ||= $site;
  my $version = $self->biogmod_version;
  my $ua  = LWP::UserAgent->new();
  $ua->agent("Bio::GMOD::Util::CheckVersions/$version");
  my $request = HTTP::Request->new('GET',$url);
  my $response = $ua->request($request);
  my %response;
  if ($response->is_success) {
    # Parse out the content
    my $content = $response->content;
    my $parsed = XMLin($content);
    foreach (keys %{$parsed}) {
      $response{$_} = $parsed->{$_};
    }
    $response{status} = "SUCCESS";