Functional test

This is a test of the GOR I protein secondary structure prediction (CNRS IBCP) service.
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This test consists of the following files:
__MACOSX/
._gbiowstest-gor1.py (binary file)
benchy_seq001.seq
>Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009) MKKITIYDLAELSGVSASAVSAILNGNWKKRRISAKLAEKVTRIAEEQGYAINRQASMLR SKKSHVIGMIIPKYDNRYFGSIAERFEEMARERGLLPIITCTRRRPELEIEAVKAMLSWQ VDWVVATGATNPDKISALCQQAGVPTVNLDLPGSLSPSVISDNYGGAKALTHKILANSAR RRGELAPLTFIGGRRATITPASVYAASTMRIASWGLACRRRIFWLPAIRKATLRTACRSG LAARRRCCRGYLLTRRYPWKGLCAGCRRWV
control-seq001.GorI
GOR I secondary structure prediction MPSA code : secondary score GOR1 >Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009) 210 4 HETC H 81 -152 46 47 S H 68 -98 40 14 K H 63 -68 25 7 K C 21 -32 6 35 S H 17 15 -38 -19 H E -11 83 -90 -75 V E -19 152 -96 -93 I E -66 148 -78 -96 G E -77 188 -23 -66 M E -114 207 -101 -38 I E -164 147 -181 7 I E -152 97 21 35 P T -167 37 155 72 K T -165 25 94 44 Y T -170 16 101 40 D T -166 -16 102 56 N T -139 29 146 78 R T -125 70 154 74 Y T -109 46 112 69 F C -111 -2 57 109 G C -64 -22 -9 105 S C 1 -33 -106 57 I C 50 -93 -140 60 A H 113 -145 -132 6 E H 194 -171 -129 -62 R H 259 -174 -148 -86 F H 281 -155 -132 -74 E H 304 -190 -107 -49 E H 314 -177 -83 -51 M H 326 -203 -45 -55 A H 287 -216 -34 -52 R H 251 -245 -2 -59 E H 192 -216 66 -42 R T 110 -167 122 24 G C 45 -47 64 90 L C -50 43 -66 100 L E -54 117 66 73 P E -76 177 117 27 I E -84 197 14 -33 I E -116 198 41 -33 T E -148 174 74 3 C T -146 83 93 57 T T -159 9 136 118 R C -159 -66 111 138 R C -109 -86 11 178 R C 11 -98 86 148 P H 103 -90 38 96 E H 165 -112 -126 -15 L H 226 -100 -187 -139 E H 280 -103 -216 -168 I H 349 -110 -227 -194 E H 381 -128 -190 -175 A H 365 -127 -180 -153 V H 321 -113 -120 -93 K H 246 -103 -90 -65 A H 203 -82 -68 -26 M H 142 -47 -71 -25 L H 91 -27 6 -25 S H 75 -45 -19 -33 W H 75 -13 -51 0 Q H 59 48 5 40 V E 50 101 81 40 D E 17 175 21 37 W E 9 248 -35 70 V E -1 243 68 125 V E 0 137 90 125 A C -61 73 93 117 T C -111 -37 100 109 G C -110 -98 100 115 A C -111 -97 13 122 T C -126 -91 -38 121 N T -37 -48 136 133 P T -15 -24 236 112 D T 28 22 140 67 K E 46 87 79 47 I E 79 118 26 30 S E 80 177 -5 -25 A E 77 153 -36 -65 L E 47 124 24 -52 C E 3 102 79 0 Q T -55 102 129 75 Q T -105 122 165 120 A C -166 128 107 129 G E -176 183 -12 135 V E -132 227 106 163 P E -146 258 158 147 T E -138 248 40 55 V E -146 209 17 26 N E -155 163 19 10 L E -175 126 36 45 D C -215 78 -56 90 L T -167 47 136 123 P T -195 -12 187 119 G C -179 3 121 135 S C -198 53 -11 105 L C -229 103 -84 115 S E -179 177 61 98 P E -184 213 111 105 S E -171 233 5 25 V E -154 227 9 12 I E -134 168 21 35 S E -130 106 96 55 D T -131 24 112 81 N T -95 -55 144 119 Y T -51 -112 132 114 G C 24 -152 77 99 G H 110 -68 -25 32 A H 176 -18 -110 -43 K H 205 67 -117 -50 A H 217 93 -131 -65 L H 179 108 -127 -93 T H 145 95 -128 -102 H H 106 52 -110 -93 K H 96 27 -81 -33 I H 92 28 -81 -5 L H 60 -3 -20 15 A H 32 -36 -18 16 N C 26 -47 -24 60 S C 15 -48 15 60 A C 6 -41 76 88 R T -14 -6 111 68 R T -4 4 116 53 R T -48 3 97 69 G C -57 15 63 66 E C -95 -2 -66 55 L C -129 12 -155 25 A E -61 57 -31 8 P E -25 103 4 15 L E 19 128 -22 -8 T E 24 131 32 4 F E 1 82 69 57 I C -61 48 107 114 G T -101 23 162 149 G C -99 34 146 168 R C -129 49 104 118 R C -165 82 90 105 A E -186 98 91 87 T C -209 92 -6 97 I E -236 108 -127 52 T E -177 77 -9 43 P E -115 57 35 35 A E -24 68 -54 40 S E 29 68 -40 30 V H 65 45 -31 14 Y H 100 17 -55 -15 A H 90 12 -62 -55 A H 71 48 -104 -40 S E 39 58 -102 -68 T E 28 83 -68 -41 M E 16 104 -24 -57 R E 46 87 9 -18 I T 45 27 50 35 A T 31 -7 141 80 S T 15 -55 91 37 W C -21 -87 -8 44 G C -18 -62 24 40 L T -15 -28 50 40 A T -55 44 84 18 C T -64 99 131 8 R T -69 109 161 28 R T -39 99 161 28 R T -34 87 124 42 I T -26 61 122 -6 F E -58 40 -14 22 W C -98 8 -216 25 L C -32 -33 -9 53 P C 13 -78 80 80 A C 51 -98 29 57 I H 66 -61 56 25 R T 73 -28 98 32 K H 73 7 55 20 A E 39 53 8 17 T E 7 68 -23 -25 L E -14 69 1 -52 R E -13 73 38 -13 T T -5 72 75 0 A T 2 64 89 23 C T -9 34 106 23 R T -26 -7 96 55 S T -41 -32 102 54 G T 12 -27 79 45 L T 40 -8 55 15 A T 38 12 65 -10 A T 11 69 86 -47 R T -9 119 121 -57 R T -39 139 171 -47 R T -78 139 224 -12 C T -123 104 244 18 C T -179 89 201 33 R T -248 68 167 19 G T -252 105 119 14 Y E -228 128 37 30 L E -208 153 39 25 L E -208 158 78 17 T T -216 139 146 13 R T -179 99 151 53 R C -185 75 104 104 Y T -122 7 321 148 P T -138 15 341 144 W T -134 22 155 72 K T -196 38 172 59 G T -163 63 124 45 L T -168 84 114 18 C T -142 47 125 40 A T -141 13 167 64 G T -53 39 144 28 C T -39 54 111 18 R T -24 89 146 -7 R T -23 90 111 7 W E -31 98 15 35 V 381 -252 Decision constants Personalized DCH 0 DCE 0 DCT 0 DCC 0 Secondary state rates: Alpha helix : 46 21.90% Beta sheet : 60 28.57% Turn : 65 30.95% Coil : 39 18.57%
gbiowstest-gor1.py
#!/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 GorI_Service_client import *
fn_input = 'benchy_seq001.seq'
fn_control = 'control-seq001.GorI'
ret = 0
# get a port proxy instance
loc = GorI_ServiceLocator()
port = loc.getGorIPort()
###
# submit a new request
# create
req = submitGorIRequest()
fp_input = open (fn_input, 'r')
req._Sequence = fp_input.read()
# call the remote method
resp = port.submitGorI(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 = checkStatusGorIRequest()
req._JobId = jobid
while status not in ('done','aborted'):
time.sleep(2)
resp = port.checkStatusGorI(req)
status = resp._Status
#print status
if status != 'done':
ret = 1
###
# get results
req = getResultsGorIRequest()
req._JobId = jobid
resp = port.getResultsGorI(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)
GorI_Service_client.py
##################################################
# file: GorI_Service_client.py
#
# client stubs generated by "ZSI.generate.wsdl2python.WriteServiceModule"
# /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/GorIWS.wsdl
#
##################################################
import urlparse, types
from ZSI.TCcompound import ComplexType, Struct
from ZSI import client
from ZSI.schema import GED, GTD
import ZSI
# Locator
class GorI_ServiceLocator:
GorIPort_address = "http://gbio.ibcp.fr:8090/GorI_Service"
def getGorIPortAddress(self):
return GorI_ServiceLocator.GorIPort_address
def getGorIPort(self, url=None, **kw):
return GorIBindingSOAP(url or GorI_ServiceLocator.GorIPort_address, **kw)
# Methods
class GorIBindingSOAP:
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: submitGorI
def submitGorI(self, request, **kw):
if isinstance(request, submitGorIRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:GorIWS.wsdl#submitGorI", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=submitGorIResponse.typecode.ofwhat, pyclass=submitGorIResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
# op: checkStatusGorI
def checkStatusGorI(self, request, **kw):
if isinstance(request, checkStatusGorIRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:GorIWS.wsdl#checkStatusGorI", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=checkStatusGorIResponse.typecode.ofwhat, pyclass=checkStatusGorIResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
# op: getResultsGorI
def getResultsGorI(self, request, **kw):
if isinstance(request, getResultsGorIRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:GorIWS.wsdl#getResultsGorI", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=getResultsGorIResponse.typecode.ofwhat, pyclass=getResultsGorIResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
# op: cancelGorI
def cancelGorI(self, request, **kw):
if isinstance(request, cancelGorIRequest) is False:
raise TypeError, "%s incorrect request type" % (request.__class__)
# no input wsaction
self.binding.Send(None, None, request, soapaction="urn:GorIWS.wsdl#cancelGorI", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw)
# no output wsaction
typecode = Struct(pname=None, ofwhat=cancelGorIResponse.typecode.ofwhat, pyclass=cancelGorIResponse.typecode.pyclass)
response = self.binding.Receive(typecode)
return response
class submitGorIRequest:
def __init__(self, **kw):
"""Keyword parameters:
Sequence -- part Sequence
"""
self._Sequence = kw.get("Sequence")
submitGorIRequest.typecode = Struct(pname=("urn:GorI_Service","submitGorI"), ofwhat=[ZSI.TC.String(pname="Sequence", aname="_Sequence", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitGorIRequest, encoded="urn:GorI_Service")
class submitGorIResponse:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
submitGorIResponse.typecode = Struct(pname=("urn:GorI_Service","submitGorIResponse"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=submitGorIResponse, encoded="urn:GorI_Service")
class checkStatusGorIRequest:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
checkStatusGorIRequest.typecode = Struct(pname=("urn:GorI_Service","checkStatusGorI"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusGorIRequest, encoded="urn:GorI_Service")
class checkStatusGorIResponse:
def __init__(self, **kw):
"""Keyword parameters:
Status -- part Status
"""
self._Status = kw.get("Status")
checkStatusGorIResponse.typecode = Struct(pname=("urn:GorI_Service","checkStatusGorIResponse"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=checkStatusGorIResponse, encoded="urn:GorI_Service")
class getResultsGorIRequest:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
getResultsGorIRequest.typecode = Struct(pname=("urn:GorI_Service","getResultsGorI"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsGorIRequest, encoded="urn:GorI_Service")
class getResultsGorIResponse:
def __init__(self, **kw):
"""Keyword parameters:
SecStructure -- part SecStructure
"""
self._SecStructure = kw.get("SecStructure")
getResultsGorIResponse.typecode = Struct(pname=("urn:GorI_Service","getResultsGorIResponse"), ofwhat=[ZSI.TC.String(pname="SecStructure", aname="_SecStructure", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=getResultsGorIResponse, encoded="urn:GorI_Service")
class cancelGorIRequest:
def __init__(self, **kw):
"""Keyword parameters:
JobId -- part JobId
"""
self._JobId = kw.get("JobId")
cancelGorIRequest.typecode = Struct(pname=("urn:GorI_Service","cancelGorI"), ofwhat=[ZSI.TC.String(pname="JobId", aname="_JobId", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelGorIRequest, encoded="urn:GorI_Service")
class cancelGorIResponse:
def __init__(self, **kw):
"""Keyword parameters:
Status -- part Status
"""
self._Status = kw.get("Status")
cancelGorIResponse.typecode = Struct(pname=("urn:GorI_Service","cancelGorIResponse"), ofwhat=[ZSI.TC.String(pname="Status", aname="_Status", typed=False, encoded=None, minOccurs=1, maxOccurs=1, nillable=True)], pyclass=cancelGorIResponse, encoded="urn:GorI_Service")
GorI_Service_client.pyc (binary file)
GorI_Service_types.py
################################################## # file: GorI_Service_types.py # # schema types generated by "ZSI.generate.wsdl2python.WriteServiceModule" # /usr/local/bin/wsdl2py http://gbio-pbil.ibcp.fr/ws/GorIWS.wsdl # ################################################## import ZSI import ZSI.TCcompound from ZSI.schema import LocalElementDeclaration, ElementDeclaration, TypeDefinition, GTD, GED
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