Functional test

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

GOR II secondary structure prediction
MPSA code : secondary score GOR2
>Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009)
210 3 HEC
C    -3  -114    57 S
C   -12  -106    67 K
C     5  -124    62 K
C     3   -53    16 S
H    25   -51   -14 H
E    14    47   -77 V
E   -23    63   -53 I
E   -70   125   -63 G
E   -84   204  -102 M
E   -82   175   -93 I
E  -191    90    26 I
E  -145    60    38 P
C  -162   -25   129 K
C  -159   -90   171 Y
C  -144  -111   152 D
C  -107  -115   135 N
C   -67  -122   113 R
C   -49    12    13 Y
E   -77    42    19 F
C   -99    11    56 G
C   -87   -33    72 S
H     5   -43    -2 I
H    76   -63   -57 A
H   112   -68   -67 E
H   147  -112   -70 R
H   199   -84  -132 F
H   196  -104  -113 E
H   229  -138  -119 E
H   195  -118  -111 M
H   233  -214   -72 A
H   280  -193  -130 R
H   265  -186  -124 E
H    76  -227    51 R
C   -67  -123    85 G
C   -91   -21    44 L
C  -210    -2   106 L
E  -115    42    24 P
E   -94    74    -6 I
E  -126   106    -1 I
E   -77    79   -12 T
E   -73   114   -30 C
C   -98    41    45 T
C  -114   -59   121 R
C  -140  -158   202 R
C  -240  -211   290 R
C   -93  -287   229 P
C    14  -219    98 E
H    40  -155    35 L
H    99  -195     3 E
H   229  -121  -147 I
H   310   -85  -241 E
H   325   -96  -252 A
H   343  -126  -240 V
H   311  -143  -191 K
H   296   -82  -211 A
H   210   -89  -133 M
H   172  -110   -71 L
H   152  -117   -63 S
H   172   -34  -129 W
H    95   -11   -88 Q
H   107   -54   -86 V
H    94    26  -138 D
E    75   101  -180 W
E    57   196  -224 V
E    62   134  -186 V
E    66    91  -146 A
C    -4   -60    19 T
C   -78  -139   121 G
C   -49  -205   135 A
C   -97  -162   146 T
C  -246  -266   298 N
C   -77  -261   174 P
C   -51  -170   100 D
C    13  -127    29 K
H    34   -34   -38 I
H    52   -19   -55 S
H    99    21  -112 A
H    73    40  -109 L
H    73    10   -87 C
H    35    -1   -48 Q
C   -17   -99    60 Q
C   -90  -130   132 A
C  -211  -139   218 G
C  -254   -96   191 V
C  -146   -33    91 P
E  -192   113    31 T
E  -183   116    26 V
E  -121    85     2 N
E   -96    37     9 L
C  -193     3   100 D
C  -263   -45   168 L
C  -170  -144   184 P
C  -237  -108   217 G
C  -231   -57   189 S
C  -226   -12   151 L
C  -333    23   198 S
C  -187    50    88 P
E  -234   156    59 S
E  -188   191   -11 V
E  -155   190   -31 I
E  -117   103   -14 S
C   -66   -10    21 D
C   -18  -103    38 N
C    -6   -98    26 Y
C     8  -141    42 G
C   -16  -139    54 G
H    93  -172   -10 A
H   146   -77  -111 K
H   179   -21  -171 A
H   177    -7  -175 L
H   203    -5  -185 T
H   202     7  -191 H
H   212    15  -203 K
H   199    10  -194 I
H   173     0  -171 L
H   102   -60   -62 A
H    67  -162    39 N
H    92  -225    46 S
H    99   -98   -30 A
H   109  -134   -15 R
H    78  -104    -8 R
H    69   -90   -19 R
H    41  -119    11 G
H    23   -20   -43 E
E   -36    11   -22 L
C  -163     8    61 A
C   -24    -9    -9 P
H    52    36   -96 L
E    47    90  -126 T
E    74   132  -172 F
E    40    84  -117 I
E   -31    46   -43 G
C   -93   -68    84 G
C  -135    15    71 R
E  -121    89    12 R
E  -163   110    23 A
E  -162   116    16 T
E  -120    67    17 I
C  -254    62    99 T
E  -116    73     7 P
E   -56    19     3 A
E   -33    34   -22 S
E    23    47   -82 V
H    49   -14   -64 Y
E    -1     6   -36 A
C     4   -61    12 A
E    37    41   -79 S
H   110    70  -158 T
H   106    86  -163 M
E    -2   117  -106 R
E    41   112  -146 I
E    35    98  -122 A
E     6    24   -54 S
C    -6   -52    10 W
C   -84   -78    79 G
H    -7   -16   -17 L
H    57    28   -94 A
H    43    24   -69 C
H    42   -29   -36 R
H    66   -67   -28 R
H    82     3   -90 R
H   119   -10  -127 I
H    77    18  -120 F
H    37    14   -84 W
C   -34   -42   -19 L
H    72  -101   -35 P
H   207   -40  -179 A
H   180  -196   -52 I
H    92  -226    32 R
H   108  -166   -16 K
H   102   -85   -54 A
E     4    23   -46 T
E    11    13   -42 L
H    26   -20   -27 R
H    60     8   -78 T
H    64    27   -98 A
H    74   -19   -74 C
H    82   -56   -51 R
C  -102  -144   144 S
C  -223  -108   208 G
C  -159   -61   125 L
C  -163    21    75 A
C  -198    62    84 A
C  -160    47    67 R
E  -147    71    40 R
E   -36   147   -89 R
E   -86   177   -77 C
E   -95    71    11 C
C  -150   -10   102 R
C  -228   -16   164 G
C  -229    82   106 Y
E  -188   111    41 L
E  -190   149    18 L
E  -207   105    68 T
C  -271    55   143 R
C  -183   -13   114 R
C  -191     0    94 Y
C  -176   -95   149 P
C  -139   -26    80 W
C  -128    -7    72 K
C  -185    61    65 G
E  -161   111    21 L
E   -97    61    12 C
C  -108   -20    72 A
C  -153   -51   121 G
C  -110   -25    80 C
C  -124     4    78 R
E  -126    63    31 R
E  -133   148   -18 W
E  -117   140   -32 V
  343
 -333
Helix :     76   36.19%
Sheet :     58   27.62%
Coil  :     76   36.19%

#!/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 GorIII_Service_client import *

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

# get a port proxy instance
loc = GorIII_ServiceLocator()
port = loc.getGorIIIPort()

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

# call the remote method
resp = port.submitGorIII(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 = checkStatusGorIIIRequest()
req._JobId = jobid
while status not in ('done','aborted'):
	time.sleep(2) 
	resp = port.checkStatusGorIII(req)
	status = resp._Status
	#print status
if status != 'done':
	ret = 1

###
# get results
req = getResultsGorIIIRequest()
req._JobId = jobid
resp = port.getResultsGorIII(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: GorIII_Service_client.py
# 
# client stubs generated by "ZSI.generate.wsdl2python.WriteServiceModule"
#     /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/GorIIIWS.wsdl
# 
##################################################


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

# Locator
class GorIII_ServiceLocator:
    GorIIIPort_address = "http://gbio.ibcp.fr:8090/GorIII_Service"
    def getGorIIIPortAddress(self):
        return GorIII_ServiceLocator.GorIIIPort_address
    def getGorIIIPort(self, url=None, **kw):
        return GorIIIBindingSOAP(url or GorIII_ServiceLocator.GorIIIPort_address, **kw)

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

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

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

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

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

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

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

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

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

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

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

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

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

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