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lib/Bio/Phylo/CIPRES.pm  view on Meta::CPAN

	my $self = shift;
	my $ua   = $self->ua;
	my $url  = $self->url;
	my $load = $self->payload;
	my @head = $self->headers(1);
	my $res  = $ua->post( $url . '/job/' . $self->user, $load, @head );
	if ( $res->is_success ) {
	
		# run submission, parse result
		my $status_url;	
		my $result = $res->decoded_content;
		DEBUG $result;
		XML::Twig->new(
			'twig_handlers' => {
				'jobstatus/selfUri/url' => sub { $status_url = $_->text }
			}
		)->parse($result);
		INFO "Job launched at $status_url";
		return $status_url;	
	}
	else {

lib/Bio/Phylo/CIPRES.pm  view on Meta::CPAN

sub check_status {
	my ( $self, $url ) = @_;
	INFO "Going to check status for $url";
	my $ua   = $self->ua;
	my @head = $self->headers(0);
	my $res  = $ua->get( $url, @head );
	if ( $res->is_success ) {
	
		# post request, fetch result
		my ( $status, $outfiles );
		my $result = $res->decoded_content;
		DEBUG $result;
		XML::Twig->new(
			'twig_handlers' => {
				'jobstatus/resultsUri/url' => sub { $outfiles = $_->text },
				'jobstatus/terminalStage'  => sub { $status   = $_->text }			
			}
		)->parse($result);
		my $time = localtime();
		INFO "[$time] completed: $status";
		return { 'completed' => $status, 'outfiles' => $outfiles };	

lib/Bio/Phylo/CIPRES.pm  view on Meta::CPAN

=cut

sub get_results {
	my ( $self, $url ) = @_;	
	my %out  = %{ $self->outfile }; 
	my $ua   = $self->ua;
	my @head = $self->headers(0);
	my $res  = $ua->get( $url, @head );
	my %out_url;
	if ( $res->is_success ) {
		my $result = $res->decoded_content;
		DEBUG $result;
		XML::Twig->new(
			'twig_handlers' => {
				'results/jobfiles/jobfile' => sub {
					my $node = $_;
					my $name = $node->findvalue('filename');
					if ( $out{ $name } ) {
						$out_url{ $name } = $node->findvalue('downloadUri/url');
					}
					DEBUG $node->toString;
				}
			}
		)->parse($result);
		for my $name ( keys %out ) {
			my $location = $out_url{ $name };
			$res = $ua->get( $location, @head );
			if ( $res->is_success ) {
				open my $fh, '>', $out{ $name } or die $!;
				print $fh $res->decoded_content;
			}
			else {
				throw 'NetworkError' => $res->status_line;	
			}
		}		
	}
	else {
		throw 'NetworkError' => $res->status_line;	
	}
}