Functional test

>Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009)
MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR
SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ
VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR
RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG
LAARRRCCRGYLLTRRYPWKGLCAGCRRWV

SIMPA96 secondary structure prediction program

H = helix b = strand . = other

Scale indicates prediction strength: 0-weak, 2-medium, 5-strong 9-very strong

secondary structure prediction without homologues

sequence 1

Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009


                    10        20        30        40        50        60
sequence    MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR
prediction  ...bbbHHHHHH...HHHHHHHHH...HHHHHHHHHHHHHHHHHHHH....HHHHHHHHH
scale       142122102211233201232221244211222345544454443312430000023443


                    70        80        90       100       110       120
sequence    SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ
prediction  H.HHHHHbbb.......HHHHHHHHHHHHHHH...bbbbb.....HHHHHHHHHHHHHH.
scale       001010001202345310002455566654422640244212223111233344443201


                   130       140       150       160       170       180
sequence    VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR
prediction  ..bbbb.....HHHHHHHHHH....bbbb.........bb......HHHHHHHHHHHHH.
scale       010230255673024433331476402101467545411114445410223433431110


                   190       200       210       220       230       240
sequence    RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG
prediction  ......bbbb............bb....bbbb......HHHHHH....HHHHHHHHHH..
scale       013310034304542110343200122101100133210000001211100122331023


                   250       260       270       280       290
sequence    LAARRRCCRGYLLTRRYPWKGLCAGCRRWVASWGLACRRRIFWLPAIRKATLRTACRSG
prediction  ...........bb...........HHHHHHHH.....HHHHHH.....HHHHHHHHH..
scale       21010012331122444222313210221120121000000001211100021121024

#!/usr/bin/env python
# ================================================================================
#
#                             COPYRIGHT NOTICE
#
#                Centre National de la Recherche Scientifique
#                                   CNRS
#
#                Institut de Biologie et Chimie des Proteines
#                             IBCP CNRS UMR 5086
#                            7 passage du Vercors
#                             69007 Lyon, FRANCE
#
#  This software/database is covered by copyright of CNRS IBCP
#  All rights reserved. Reproduction and usage of this software/database are 
#  strictly restricted, and need a prior written permission from CNRS IBCP
#  (see "Contact" below).
#
#  CNRS IBCP do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. CNRS IBCP disclaim all
#  warranties, express or implied, including warranties of performance,
#  merchantability or fitness for any particular purpose.
#
# ================================================================================
#
# Author: Christophe Blanchet
#
# Contact: Christophe.Blanchet@ibcp.fr
#
# First Version Creation Date:   18/11/2008
#
# $Revision: 1.0 $
#
# File Description: 
#
#
# Modifications:
# --------------------------------------------------------------------------
# Date     Name        Description of modification
# -------  ----------  -----------------------------------------------------
#
# ================================================================================
import sys
import time
from Simpa96_Service_client import *

fn_input = 'benchy_seq001.seq'
fn_control = 'control-seq001.Simpa96'
ret = 0

# get a port proxy instance
loc = Simpa96_ServiceLocator()
port = loc.getSimpa96Port()

###
# submit a new request
# create
req = submitSimpa96Request()
fp_input = open (fn_input, 'r')
req._Sequences = fp_input.read()

# call the remote method
resp = port.submitSimpa96(req)
jobid = resp._JobId
#print jobid
if not jobid:
	ret = 1

###
# check status
# while status different of 'done' or 'aborted', check again
status = 'init'
req = checkStatusSimpa96Request()
req._JobId = jobid
while status not in ('done','aborted'):
	time.sleep(2) 
	resp = port.checkStatusSimpa96(req)
	status = resp._Status
	#print status
if status != 'done':
	ret = 1

###
# get results
req = getResultsSimpa96Request()
req._JobId = jobid
resp = port.getResultsSimpa96(req)

# write result
#open(fn_control,'w').write(resp._SecStructure)

#compare result with ref
resultcontrol = open(fn_control, 'r').read()
if resp._SecStructure != resultcontrol:
	ret = 1
	#print "wooohh"

#print ret
sys.exit (ret)

##################################################
# file: Simpa96_Service_client.py
# 
# client stubs generated by "ZSI.generate.wsdl2python.WriteServiceModule"
#     /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/Simpa96WS.wsdl
# 
##################################################


import urlparse, types
from ZSI.TCcompound import ComplexType, Struct
from ZSI import client
from ZSI.schema import GED, GTD
import ZSI

# Locator
class Simpa96_ServiceLocator:
    Simpa96Port_address = "http://gbio.ibcp.fr:8090/Simpa96_Service"
    def getSimpa96PortAddress(self):
        return Simpa96_ServiceLocator.Simpa96Port_address
    def getSimpa96Port(self, url=None, **kw):
        return Simpa96BindingSOAP(url or Simpa96_ServiceLocator.Simpa96Port_address, **kw)

# Methods
class Simpa96BindingSOAP:
    def __init__(self, url, **kw):
        kw.setdefault("readerclass", None)
        kw.setdefault("writerclass", None)
        # no resource properties
        self.binding = client.Binding(url=url, **kw)
        # no ws-addressing

    # op: submitSimpa96
    def submitSimpa96(self, request, **kw):
        if isinstance(request, submitSimpa96Request) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:Simpa96WS.wsdl#submitSimpa96", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=submitSimpa96Response.typecode.ofwhat, pyclass=submitSimpa96Response.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

    # op: checkStatusSimpa96
    def checkStatusSimpa96(self, request, **kw):
        if isinstance(request, checkStatusSimpa96Request) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:Simpa96WS.wsdl#checkStatusSimpa96", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=checkStatusSimpa96Response.typecode.ofwhat, pyclass=checkStatusSimpa96Response.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

    # op: getResultsSimpa96
    def getResultsSimpa96(self, request, **kw):
        if isinstance(request, getResultsSimpa96Request) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:Simpa96WS.wsdl#getResultsSimpa96", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=getResultsSimpa96Response.typecode.ofwhat, pyclass=getResultsSimpa96Response.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

    # op: cancelSimpa96
    def cancelSimpa96(self, request, **kw):
        if isinstance(request, cancelSimpa96Request) is False:
            raise TypeError, "%s incorrect request type" % (request.__class__)
        # no input wsaction
        self.binding.Send(None, None, request, soapaction="urn:Simpa96WS.wsdl#cancelSimpa96", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
        # no output wsaction
        typecode = Struct(pname=None, ofwhat=cancelSimpa96Response.typecode.ofwhat, pyclass=cancelSimpa96Response.typecode.pyclass)
        response = self.binding.Receive(typecode)
        return response

class submitSimpa96Request:
    def __init__(self, **kw):
        """Keyword parameters:
        Sequences -- part Sequences
        """
        self._Sequences =  kw.get("Sequences")
submitSimpa96Request.typecode = Struct(pname=("urn:Simpa96_Service","submitSimpa96"), ofwhat=[ZSI.TC.String(pname="Sequences", aname="_Sequences", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitSimpa96Request, encoded="urn:Simpa96_Service")

class submitSimpa96Response:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
submitSimpa96Response.typecode = Struct(pname=("urn:Simpa96_Service","submitSimpa96Response"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitSimpa96Response, encoded="urn:Simpa96_Service")

class checkStatusSimpa96Request:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
checkStatusSimpa96Request.typecode = Struct(pname=("urn:Simpa96_Service","checkStatusSimpa96"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusSimpa96Request, encoded="urn:Simpa96_Service")

class checkStatusSimpa96Response:
    def __init__(self, **kw):
        """Keyword parameters:
        Status -- part Status
        """
        self._Status =  kw.get("Status")
checkStatusSimpa96Response.typecode = Struct(pname=("urn:Simpa96_Service","checkStatusSimpa96Response"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusSimpa96Response, encoded="urn:Simpa96_Service")

class getResultsSimpa96Request:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
getResultsSimpa96Request.typecode = Struct(pname=("urn:Simpa96_Service","getResultsSimpa96"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsSimpa96Request, encoded="urn:Simpa96_Service")

class getResultsSimpa96Response:
    def __init__(self, **kw):
        """Keyword parameters:
        SecStructure -- part SecStructure
        Logout -- part Logout
        """
        self._SecStructure =  kw.get("SecStructure")
        self._Logout =  kw.get("Logout")
getResultsSimpa96Response.typecode = Struct(pname=("urn:Simpa96_Service","getResultsSimpa96Response"), ofwhat=[ZSI.TC.String(pname="SecStructure", aname="_SecStructure", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True), ZSI.TC.String(pname="Logout", aname="_Logout", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsSimpa96Response, encoded="urn:Simpa96_Service")

class cancelSimpa96Request:
    def __init__(self, **kw):
        """Keyword parameters:
        JobId -- part JobId
        """
        self._JobId =  kw.get("JobId")
cancelSimpa96Request.typecode = Struct(pname=("urn:Simpa96_Service","cancelSimpa96"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelSimpa96Request, encoded="urn:Simpa96_Service")

class cancelSimpa96Response:
    def __init__(self, **kw):
        """Keyword parameters:
        Status -- part Status
        """
        self._Status =  kw.get("Status")
cancelSimpa96Response.typecode = Struct(pname=("urn:Simpa96_Service","cancelSimpa96Response"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelSimpa96Response, encoded="urn:Simpa96_Service")

##################################################
# file: Simpa96_Service_types.py
#
# schema types generated by "ZSI.generate.wsdl2python.WriteServiceModule"
#    /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/Simpa96WS.wsdl
#
##################################################

import ZSI
import ZSI.TCcompound
from ZSI.schema import LocalElementDeclaration, ElementDeclaration, TypeDefinition, GTD, GED