KBWS SOAP Service is the proxy web service to access Keio Bioinformatics Web Service (KBWS) via SOAP service. Detail documentation about KBWS is available from here.

- RPC/Encoded http://soap.g-language.org/kbws.wsdl

- Document/Literal http://soap.g-language.org/kbws_dl.wsdl

using SOAP::Lite (0.60)

#!/usr/bin/perl
use SOAP::Lite;
 
my $seq = `cat test.fasta`;
 
my $soap  = SOAP::Lite->service("http://soap.g-language.org/kbws.wsdl");
my $inputParams = SOAP::Data->name("params")->type(map => { "d" => "swissprot" });
 
my $jobid = $soap->runBlast($seq, $inputParams);
 
sleep 3 while ( $soap->checkStatus($jobid) == 0 );
 
print $soap->getResult($jobid);

using soap4r

#!/usr/bin/env ruby
require 'KBWSDriver.rb'
 
# create WSDL driver
endpoint_url = ARGV.shift
obj = KBWS.new(endpoint_url)
 
# input sequence data (fasta format)
file = open("test.fasta")
parameters = { "in0" => file.read, "params" => { "d" => "swissprot" } }
 
# run your job
jobid = obj.runBlast( parameters )
 
print jobid.s_gensym3
 
# polling your job
while obj.checkStatus( jobid ).s_gensym3 == 0
   sleep 3
end
 
# get result
puts obj.getResult( jobid ).s_gensym3

using SOAPpy

#!/usr/bin/python
 
from SOAPpy import WSDL
 
# create WSDL driver
wsdl = 'http://soap.g-language.org/kbws.wsdl'
serv = WSDL.Proxy(wsdl)
 
# input sequence data (fasta format)
for line in open('test.fasta','r')
   file + line
 
# run your job
jobid = serv.runGlimmer(file,'')
 
# polling your job
status = serv.checkStatus(jobid)
while status == 0:
   sleep(3)
   status = serv.checkStatus(jobid)
 
# get result
results = serv.getResult(jobid)
 
print results

using Apache Axis (>1.4)

import java.io.*;
import kbws.*;
 
class runBlast {
    public static void main(String[] args) throws Exception {
        KBWSServiceLocator  locator = new KBWSServiceLocator();
        KBWS_PortType serv    = locator.getKBWS();
 
        FileReader in = new FileReader("/home/kbws/test.fasta");
        BufferedReader br = new BufferedReader(in);
 
        String in0 = "";
        String line;
        while ((line = br.readLine()) != null) {
            in0 = in0 + line + "\n";
        }
 
        BlastInputParams parameter = new BlastInputParams();
        parameter.setD("swissprot");
 
        System.out.println (serv.runBlast( in0, parameter ) );
    }
}

use SOAP::Lite (0.712)

#!/usr/bin/env perl
use SOAP::Lite;
use MIME::Base64;
 
use strict;
use warnings;
 
my $soap = SOAP::Lite->new( proxy => 'http://soap.g-language.org/kbws/kbws.cgi');
$soap->autotype(0);
$soap->default_ns('urn:KBWS');
 
my $seq = `cat test.fasta`;
$seq = encode_base64($seq);
 
my %param = (
             d => "swissprot",
            );
 
my $blast = $soap->on_action( sub{"urn:KBWS#runBlast"} );
 
my $jobid = $blast->runBlast(
                             SOAP::Data->name('in0')->value($seq),
                             SOAP::Data->name('params')->value(%param),
                            )->result();
 
print "jobid : ".$jobid."\n";
 
my $poll = $soap->on_action( sub{"urn:KBWS#checkStatus"} );
sleep 3 while ( $poll->checkStatus( SOAP::Data->name('jobid')->value($jobid) )->result() == 0 );
 
print $soap->on_action( sub{"urn:KBWS#getResult"} )->getResult( SOAP::Data->name('jobid')->value($jobid) )->result();

using soap4r
 
#!/usr/bin/env ruby
require 'KBWSDriver.rb'
 
endpoint_url = ARGV.shift
obj = KBWS.new(endpoint_url)
 
# run ruby with -d to see SOAP wiredumps.
obj.wiredump_dev = STDERR if $DEBUG
 
file = open("test.fasta")
parameters = { "in0" => file.read, "params" => {"d" => "swissprot" } }
 
jobid = obj.runBlast( parameters )
 
print jobid.s_gensym3
 
while obj.checkStatus( jobid ).s_gensym3 == 0
   sleep 3
end
 
puts obj.getResult( jobid ).s_gensym3

require Apache Axis (>1.4)

import java.io.*;
import kbws.*;
 
class runBlast {
    public static void main(String[] args) throws Exception {
        KBWS_ServiceLocator  locator = new KBWS_ServiceLocator();
        KBWS_PortType serv    = locator.getKBWSHttpPort();
 
        FileReader in = new FileReader("/home/kbws/test.fasta");
        BufferedReader br = new BufferedReader(in);
 
        String in0 = "";
        String line;
        while ((line = br.readLine()) != null) {
            in0 = in0 + line + "\n";
        }
 
        BlastInputParams parameter = new BlastInputParams();
        parameter.setD("swissprot");
 
        String jobid = serv.runBlast( in0, parameter );
        System.out.println ( jobid );
 
        while ( serv.checkStatus( jobid ) == 0 ) {
            Thread.sleep(3000);
        }
 
        System.out.println( serv.getResult( jobid ) );
 
    }
}