G::Tools WebServices
SummaryIncluded librariesPackage variablesDescriptionGeneral documentationMethods
Summary
    G::Tools::WebServices - Interface to web services, including BioMOBY and TogoWS
Package variables
No package variables defined.
Included modules
G::Messenger
LWP::Simple
SelfLoader
SubOpt
Inherit
Exporter
Synopsis
No synopsis!
Description
    This class is a part of G-language Genome Analysis Environment, 
    collecting interfaces to web services.
Methods
keggapiDescriptionCode
togoWSDescriptionCode
wsDescriptionCode
Methods description
keggapicode    nextTop
 Name: keggapi   -   runs KEGG API

 Description:
    This is a wrapper around KEGG API REST wrapper, provided at
    http://rest.g-language.org/keggapi/.

    Refer to the official KEGG API web site for detailed documentations.
    http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
    
 Usage:
    ex. 
    @list_of_services = keggapi();

    @list_of_pathways = keggapi('get_pathways_by_compounds', 'C00668');
    #Note that cpd: for compound ID is optional. Likewise for ec:, gl:, dr:

 Options:
    None.

 Author: 
    Kazuharu Arakawa (gaou@sfc.keio.ac.jp)

 History:
   20100123-01 initial posting
togoWScodeprevnextTop
 Name: togoWS   -   runs togoWS REST web services

 Description:
    This is a wrapper around togoWS REST web services provided at
    http://togows.dbcls.jp/.
    
 Usage:
    #search
    @ids = togoWS(-search=>"keyword", -db=>"database");

    #entry
    $entry = togoWS(@ids);

 Options:
    -search  required option for keyword searching. 
    -db      name of the database for searching and entry retrieval
             required for searching, but not required for entry 
             retrieval, since corresponding database is automatically
             selected from the ID format. However, majority of the 
             databases simply use large numbers as IDs, which all
             result in "pubmed" as the databases. Therefore, use 
             of this option is necessary for IDs that are only numbers.
    -field   field name for entry retrieval (optional)
    -format  format name for entry retrieval (optional)

 Author: 
    Kazuharu Arakawa (gaou@sfc.keio.ac.jp)

 History:
   20090313-01 initial posting
wscodeprevnextTop
 Name: ws   -   runs web services through BioMOBY

 Description:
    This is a wrapper around MOBY::Client::Service to run web services
    through BioMOBY. Use help -w  to search for web services,
    help -w  to view service description. 
    
 Usage:
    ws(, $argument1=>$ontology_or_namespace, ...);

    arguments are given as hash, where the key is the argument and the 
    value is the MOBY ontology or Namespace.

    ex: 
      ws('MOBYSHoundGetGenBankWhateverSequence', 'EX5B_ECOLI'=>'Swiss-Prot')

 Options:
    None.  

 References:
   1. Wilkinson MD, Links M (2002) "BioMOBY: an open source biological web services
      proposal.", Brief Bioinform., 3(4):331-341.
   2. Wilkinson M, Schoof H, Ernst R, Haase D (2005) "BioMOBY successfully integrates 
      distributed heterogeneous bioinformatics Web Services. The PlaNet exemplar case.",
      Plant Physiol., 138(1):5-17.

 Author: 
    Kazuharu Arakawa (gaou@sfc.keio.ac.jp)

 History:
   20080227-01 initial posting
Methods code
keggapidescriptionprevnextTop
sub keggapi {
    my $program = shift;
    return readFile('http://rest.g-language.org/keggapi/' . $program . '/' . join('/', @_), 1);
}
togoWSdescriptionprevnextTop
sub togoWS {
    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] =~ /^NC_\d+$/){
		$opt{db} = 'genbank';
	    }elsif($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';
	    }
	}

	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);
    }
}
wsdescriptionprevnextTop
sub ws {
    my $service = shift;

    require MOBY::Client::Central;
    require MOBY::Client::Service;
    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;
    }
}
General documentation
No general documentation available.