#!/usr/bin/python
# Description: Client script in Python (suds) 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

from suds.client import Client
from suds.bindings import binding
import logging
logging.basicConfig(level=logging.INFO)
logging.getLogger('suds.client').setLevel(logging.DEBUG)
wsdl = 'http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws1.wsdl'
client = Client(wsdl,cache=None)

#runService --You need to change the sequences and ids as per your requirement. 
	      #organism and method are optional as per wsdl document
	      
	seq1 = client.factory.create('runService.parameters.sequencedata.sequence')
	seq1.id="IPI:IPI00000005.1"
	seq1.seq="""MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
		    QEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDL
		    PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG
		    CMGLPCVVM"""

	seq2 = client.factory.create('runService.parameters.sequencedata.sequence')
	seq2.id="IPI:IPI00000013.1";
	seq2.seq="""MNLSLVLAAFCLGIASAVPKFDQNLDTKWYQWKATHRRLYGANEEGWRRAVWEKNMKMIE
		    LHNGEYSQGKHGFTMAMNAFGDMTNEEFRQMMGCFRNQKFRKGKVFREPLFLDLPKSVDW
		    RKKGYVTPVKNQKQCGSCWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNG
		    GFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVANDTGFTVVAPGKEKALMKAV
		    ATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSNNSKYWLVK
		    NSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV"""

	request=client.factory.create('runService.parameters')
	request.sequencedata.sequence=[seq1,seq2]
	response = client.service.runService(request)

#pollQueue  --jobid needs to be changed as which you got from runService
	
	seq = client.factory.create('pollQueue.job')
	seq.jobid="5DBA18D0-3C44-11E1-BD82-8CB1A79C20B1"
	response = client.service.pollQueue(seq)

#fetchResults --jobid needs to be changed as which you got from runService
 
	seq = client.factory.create('fetchResult.job')
	seq.jobid="D75E7706-7279-11E1-864F-F32F2EB4B995"
	response = client.service.fetchResult(seq)

### client code ends here

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

#	Introduction:

#		Suds are very pythonic, and easy to create WSDL-consuming SOAP clients. The Suds web 
#		services client is a lightweight soap-based client. 
#		Basic features are: no class generation, provides an object-like API.,reads wsdl at 
#	        runtime for encoding/decoding and provides SOAP(style) binding/encoding.

#	Installation:

#		Required/Tested version: Python v2.6 and Suds -v 0.4

#		Download and install suds on Linux with these following commands

#		 * wget suds
#		 * tar -zxvf python-suds-0.4.tar.gz
#		 * cd python-suds-0.4
#		 * sudo python setup.py install

#	Implementation:

#		The library is now ready to use. We start by importing the suds library, creating a client 
#		based on a WSDl url, and asking the library to do process for the SOAP web service methods 
#		that are available to us. 

#	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:

#		Save above client code under name client.py and compile client with this command on Linux
#		(make sure that you are in same directory).

#		 >python client.py

#	Results:

#		We can see SOAP envelope request/response through logging.DEBUG while compile the code. 
#		The response from suds is based on debug level since we are using Python standard 
#		lib logging package for input/output. Once the console handler is configured, enabled 
#		module specific debugging doing the following: 
#		logging.getLogger('suds.client').setLevel(logging.(logging.DEBUG). 
#		It is useful when debugging a client to be able to see the actual SOAP messages exchanged.