G::Tools::WebServices - Interface to web services, including BioMOBY and TogoWS

    This class is a part of G-language Genome Analysis Environment, 
    collecting interfaces to web services.

    warn("This method is deprecated. Use emboss('kblast') instead.");
    emboss('kblast', @_);

    opt_default();
    my @args = opt_get(@_);
    my $program = shift;

    my @argv;
    my %file;
    my $i = 1;

    for my $tmp (@args){
	if(-e $tmp){
	    $file{"file$i"} = [$tmp];
	    $i ++;
	}else{
	    push(@argv, $tmp);
	}
    }

    my %options = opt_val();

    foreach my $key (keys %options){
	if ($options{$key} eq '1'){
	    push(@argv, '-' . $key);
	}else{
	    push(@argv, $key . '=' . $options{$key});
	}
    }

    require LWP::UserAgent;
    my $ua = LWP::UserAgent->new;
    my $response = $ua->post("http://rest.g-language.org/emboss/",
			     Content_Type=>'multipart/form-data',
			     Content=>[ %file, 'arg'=>join('/', @argv)]
			     );

    if ($response->is_redirect) {
	return $response->header('Location');
    }elsif ($response->is_success) {
	return $response->content;
    }else{
    	die $response->status_line;
    }

    my $program = shift;
    return readFile('http://rest.g-language.org/keggapi/' . $program . '/' . join('/', @_), 1);

    warn("This method is deprecated. Use emboss() instead.");
    emboss('seqret', @_);

    opt_default(db=>'', format=>'', field=>'', search=>'');
    my @args = opt_get(@_);
    my %opt = opt_val();

    if(length $opt{search}){
	$opt{db} = 'uniprot' unless(length $opt{db});
	return split(/\n/, get('http://togows.dbcls.jp/search/' . $opt{db} . '/' . $opt{search}));
    }else{
	unless(length $opt{db}){
	    if($args[0] =~ /^K\d+$/){
		$opt{db} = 'orthology';
	    }elsif($args[0] =~ /^\d\.\d+\.\d+\.\d+$/){
		$opt{db} = 'enzyme';
	    }elsif($args[0] =~ /^C\d+$/){
		$opt{db} = 'compound';
	    }elsif($args[0] =~ /^D\d+$/){
		$opt{db} = 'drug';
	    }elsif($args[0] =~ /^G\d+$/){
		$opt{db} = 'glycan';
	    }elsif($args[0] =~ /^R\d+$/){
		$opt{db} = 'reaction';
	    }elsif($args[0] =~ /^[A-Z][A-Z]_\d+$/){
		$opt{db} = 'nuccore';
	    }elsif($args[0] =~ /^BIOMD\d+$/){
		$opt{db} = 'biomodels';
	    }elsif($args[0] =~ /^MODEL\d+$/){
		$opt{db} = 'biomodels';
	    }elsif($args[0] =~ /^GO:\d+$/){
		$opt{db} = 'go';
	    }elsif($args[0] =~ /^IPR\d+$/){
		$opt{db} = 'interpro';
	    }elsif($args[0] =~ /^REACT_\d+$/){
		$opt{db} = 'reactome';
	    }elsif($args[0] =~ /^[a-zA-Z0-9]+_[a-zA-Z0-9*]+$/){
		$opt{db} = 'uniprot';
	    }else{
		$opt{db} = 'pubmed';
	    }
	}

	@args = readFile('http://rest.g-language.org/gbp/wild.pl?id=' . $args[0], 1) if($args[0] =~ /\*/);

	my $url = 'http://togows.dbcls.jp/entry/' . $opt{db} . '/' . join(',', @args);
	$url .= '/' . $opt{field} if (length $opt{field});
	$url .= '.' . $opt{format} if (length $opt{format});

	return get($url);
    }

    my $service = shift;

    eval{
	require MOBY::Client::Central;
	require MOBY::Client::Service;
    };
    if($@){
	croak "MOBY::Client::Central does not seem to be installed. Try'cpan MOBY::Client::Central' to install this module to enable BioMOBY support.";
    }

    my $m = MOBY::Client::Central->new();
    my %ns = %{$m->retrieveNamespaces()};

    my ($sv, $reg) = $m->findService(serviceName=>$service);
    die("Web Service: $service not found.") unless($sv);

    my @inputlist;
    my %hash = @_;
    
    foreach my $input (@{$$sv[0]->{input}}){
	my ($query, $name) = each %hash;
	last unless($query);

	my $article = $input->articleName();
	my $xml = ($ns{$name}) ? '<Object id="'.$query.'" namespace="'.$name.'"/>' : '<'.$name.' id="'.$query.'"/>';
	push(@inputlist, [$article, $xml]);
    }

    my $wsdl = $m->retrieveService($$sv[0]);
    my $serv = MOBY::Client::Service->new( service => $wsdl );
    my $result =  $serv->execute(XMLinputlist => [@inputlist]);

    $result =~ s/\n/=%=/g;

    if($result =~ /<moby:Simple.*?>(.*)<\/moby:Simple>/){
	my $res = $1;
	$res =~ s/=%=/\n/g;
	return $res;
    }