comparison supported-motif-databases_soap.py @ 24:8e5a92e5917e draft

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24:8e5a92e5917e

#! /usr/bin/python
# -*- coding: utf8 -*-

"""#supported motif databases soap - developed by Jocelyn Brayet <[e-mail]>
#Copyright (C) 2015  Institut Curie
#
#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#This program is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
###########################################################'
# 
#Recup motif databases to each RSAT server and create loc files for Galaxy.
#
###########################################################'
# 
# List RSAT suppported motif databases.
#
#
#usage: supported-motif-databases_soap.py [-h] -galaxyPath <GALAXY_PATH>
#
#optional arguments:
#  -h, --help            show this help message and exit
#  -galaxyPath <GALAXY_PATH>, --galaxyPath <GALAXY_PATH>
#                        Galaxy tool_data_path directory (e.i. /myGalaxy
#                        /galaxy-dist/tool-data)
#
#Version 0.1 - 27/05/2015
# 
###########################################################'"""
__author__ =  'Jocelyn Brayet'
supportedMotifDatabasesVersion = '0.1 - 27/05/2015'

###########################################################'
## Import

import argparse
import os
import urllib
from suds.client import Client
import platform

###########################################################'

################################ functions ############################################################
## Define a function to make a service perform the desired request using provided arguments
def call_run_service(rsat_service, args):
	"""
	Run job in RSAT server.
		service -> RSAT web service
		args -> web service request 	 
	"""
	
	result = rsat_service.supported_motif_databases(args)
	return result

def testNone(argument):
	"""
	Test if argument is None or not.
		argument -> argument give by user
	"""

	if not argument is None:
		variable = argument[0]
	else:
		variable = ""
	return variable

def recupMotifDatabases(srv,request,dicServ):

	"""
	Recup RSAT organisms in each RSAT server.
		srv -> server key in server dictionary	
		request -> job request
		dicServ -> server dictionary
	"""

	# Create the client
	client = Client(serverDict[srv])
	# Need service interface to perform requests
	rsat_service = client.service

	print client
	# Define client header

	userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
	    supportedMotifDatabasesVersion, 
	    os.path.basename( __file__ ),
	    platform.python_version(), 
	    platform.system()
	)

	httpHeaders = {'User-agent': userAgent}
	client.set_options(headers=httpHeaders)
	client.set_options(timeout=300)

	result = call_run_service(rsat_service, request)

	###########################################################'
	## Display request results

	print '###############################################'
	print 'Command performed on server'
	print ''
	print result.command
	print ''
	print '###############################################'
	print 'Result'
	print ''
	print result.client

	return(result.client)

###########################################################'

###########################################################'
# server dictionary
serverDict = {
    
    #http://protists.rsat.eu/
    "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
    "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
    "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
    "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
    "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
    "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
    
    }


if __name__ == '__main__':

	# Create the parser
	parser = argparse.ArgumentParser(description='List RSAT suppported motif databases.', epilog='Version '+supportedMotifDatabasesVersion)

	# List desired arguments
	#parser.add_argument('-r', '--return_param', metavar='<RETURN_PARAM>', type=str, nargs=1, help='Return fields. Supported: name,format,file,descr,version,url.', required=True)
	parser.add_argument('-galaxyPath', '--galaxyPath', metavar='<GALAXY_PATH>', type=str, nargs=1, help='Galaxy tool_data_path directory (e.i. /myGalaxy/galaxy-dist/tool-data)', required=True)

	# Parse command line
	args = parser.parse_args()

	# Get values to be used
	#output_return = testNone(args.return_param)
	galaxyPath = testNone(args.galaxyPath)

	for srv in serverDict:

		functionResult=""
		reslutsTab=list()
		finalTab=list()

		supportedMotifDatabasesRequest = {
    
	    		'output' : 'client',
	    		'return' : 'name'
    
		}
		
		functionResult=recupMotifDatabases(srv,supportedMotifDatabasesRequest,serverDict)
		reslutsTab=str(functionResult).split("\n")
		del reslutsTab[-1]
		resultsFile = open(galaxyPath+"/"+"RSAT_motif_databases_"+srv+".loc","w")
		for value in reslutsTab:
			if not value.startswith("#"):
				resultsFile.write(value+"\n")
		resultsFile.close()