#!/usr/bin/php
# Description: Client script in PHP running the RNAmmer Web Service
# Author: Karunakar Bayyapu
# Email: karun@cbs.dtu.dk
# Version: 1.2 ws1
# Date: 2012-04-23
### for installation and usage notes please see below

### client code starts here

<?php
$wsdl="http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws1.wsdl";

$client = new SoapClient($wsdl,array('trace'=>1));

 #runService --You need to change the sequences and ids as per your requirement. 
	       #organism and method are optional as per wsdl document  
	    
$param = array(
        	'parameters'=>array('sequencedata'=>array(
 				'sequence'=> array(
	  			  array('id' => 'IPI:IPI00000021.5',
	    			 'seq'=> 'GAASRKRPPPALWARTPGWAFGGHTGPAAPSRRTTEAPGPNTSCRPTPQTTCGPGPGHLV
					  PARMTVRGTDGAPAYSIYGRPRRSAPFLTPGPGRYFPERAGNATYPSAPRHTIAPRNWGV
					  QAEQQSPGPAAYTVPSLLGPRVIGKVSAPTCSIYGRRAAGSFFEDLSKTPGPCAYQVVSP
					  GVYKSRAPQFTILARTSLPQDNTRKPGPAAYNVDQHRKPRGWSFGIRHSDYLAPLVTDAD
					  N'),
 	    			  array('id' => 'IPI:IPI00000013.1',
	    			  'seq'=> 'MNLSLVLAAFCLGIASAVPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIE
					   LHNGEYSQGKHGFTMAMNAFGDMTNEEFRQMMGCFRNQKFRKGKVFREPLFLDLPKSVDW
					   RKKGYVTPVKNQKQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNG
					   GFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVANDTGFTVVAPGKEKALMKAV
					   ATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSNNSKYWLVK
					   NSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV')		    		    
 						  )
					      )
			           )
	     );
$result = $client->runService($param);
echo("\nDumping request headers:\n".$client->__getLastRequestHeaders());
echo("\nDumping request:\n".$client->__getLastRequest());
echo("\nDumping response headers:\n".$client->__getLastResponseHeaders());
echo("\nDumping response:\n".$client->__getLastResponse());

#pollQueue  --jobid needs to be changed as which you got from runService

$param=array('job'=>array('jobid'=>'7BC44408-4041-11E1-AF58-C0FF935B49F0'));
$result=$client->pollQueue($param); 
echo("\nDumping request headers:\n".$client->__getLastRequestHeaders());
echo("\nDumping request:\n".$client->__getLastRequest());
echo("\nDumping response headers:\n".$client->__getLastResponseHeaders());
echo("\nDumping response:\n".$client->__getLastResponse());

#fetchResult  --jobid needs to be changed as which you got from runService

$param=array('job'=>array('jobid'=>'3D996364-727A-11E1-864F-F32F2EB4B995'));
$request=$client->fetchResult($param); 
echo("\nDumping request headers:\n".$client->__getLastRequestHeaders());
echo("\nDumping request:\n".$client->__getLastRequest());
echo("\nDumping response headers:\n".$client->__getLastResponseHeaders());
echo("\nDumping response:\n".$client->__getLastResponse());

?> 

### client code ends here

#########################################################################################
#############################				    #############################
#############################          DOCUMENTATION        #############################
#############################          			    #############################
#########################################################################################

#	Introduction:

#		To create a SOAP client to access CBS web services is easy and no need to install any 
#		extra libraries while you use PHP newer versions

#	Installation:

#		Required/tested version : PHP 5.2.14

#		You can download PHP from php.net/downloads.php or you can activate on your linux machine

#	Access Web sevices:

#		Ths RNAmmer service code access to see one method results at once. If you would like to 
#		see runService method results then you would need to comment the rest of the methods code 
#		and for rest also same. In the runService, you need to submit required fileds like one id 
#		and corresponding sequence or more ids and their corresponding sequences as a input(STDIN) 
#		data to convert FASTA format to get the results.
#		For input data/FASTA format see example: 
#			http://www.cbs.dtu.dk/ws/RNAmmer/examples/example)

#		After getting jobid from runService then you would need to submit jobid in the pollQueue 
#		to know the status of the job. After knowing the status of the job from pollQueue then 
#		you need to submit jobid in the fetchResult to see complete final results. 
#		It means you can only see final results in the fetchResult since RNAmmer is implemented 
#		in asynchronous way

#	Compile:

#		Once you saved client code in your local machine, run this command at the same time you make sure
#t		hat you are in the same directory.

#		>php client.php

#	Results:

#		We can see SOAP Request and Response with header since we are dumping headers also