Functional test

This is a test of the GOR IV protein secondary structure prediction (CNRS IBCP) service.

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Support reference#270-279

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This test consists of the following files:

__MACOSX/

benchy_seq001.seq

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

control-seq001.GorIV

Unknow sequence for GBIO Web Services test ( C Blanchet, 14 jan 2009)
270
SEQ PRD   H     E     C
 M   C  0.000 0.002 0.998
 K   C  0.000 0.015 0.985
 K   C  0.000 0.238 0.762
 I   E  0.000 0.698 0.302
 T   E  0.000 0.900 0.100
 I   E  0.002 0.940 0.058
 Y   E  0.013 0.763 0.224
 D   E  0.079 0.527 0.394
 L   H  0.559 0.197 0.244
 A   H  0.506 0.203 0.292
 E   H  0.581 0.153 0.265
 L   H  0.498 0.087 0.415
 S   C  0.299 0.116 0.585
 G   C  0.310 0.097 0.593
 V   C  0.383 0.093 0.525
 S   H  0.519 0.099 0.381
 A   H  0.674 0.081 0.245
 S   H  0.638 0.120 0.242
 A   H  0.656 0.171 0.173
 V   H  0.511 0.373 0.116
 S   H  0.441 0.437 0.122
 A   H  0.590 0.324 0.086
 I   H  0.433 0.473 0.093
 L   H  0.638 0.189 0.173
 N   H  0.525 0.033 0.441
 G   C  0.333 0.054 0.613
 N   C  0.315 0.007 0.678
 W   H  0.587 0.010 0.403
 K   H  0.635 0.031 0.334
 K   H  0.698 0.052 0.250
 R   H  0.726 0.088 0.187
 R   H  0.776 0.105 0.119
 I   H  0.701 0.151 0.148
 S   H  0.664 0.131 0.204
 A   H  0.779 0.096 0.125
 K   H  0.807 0.040 0.153
 L   H  0.798 0.039 0.164
 A   H  0.806 0.019 0.176
 E   H  0.811 0.022 0.167
 K   H  0.812 0.025 0.163
 V   H  0.833 0.036 0.130
 T   H  0.751 0.094 0.155
 R   H  0.767 0.116 0.117
 I   H  0.772 0.130 0.098
 A   H  0.812 0.072 0.115
 E   H  0.794 0.040 0.166
 E   H  0.737 0.039 0.224
 Q   H  0.671 0.026 0.303
 G   H  0.632 0.043 0.325
 Y   H  0.667 0.099 0.233
 A   H  0.593 0.205 0.202
 I   H  0.677 0.205 0.118
 N   H  0.715 0.132 0.153
 R   H  0.762 0.101 0.137
 Q   H  0.878 0.042 0.079
 A   H  0.850 0.067 0.084
 S   H  0.746 0.148 0.107
 M   H  0.767 0.094 0.139
 L   H  0.756 0.120 0.123
 R   H  0.693 0.104 0.203
 S   H  0.502 0.183 0.315
 K   H  0.496 0.106 0.398
 K   H  0.436 0.134 0.430
 S   C  0.360 0.231 0.410
 H   E  0.327 0.343 0.331
 V   E  0.176 0.624 0.201
 I   E  0.170 0.671 0.158
 G   E  0.082 0.734 0.183
 M   E  0.082 0.664 0.254
 I   E  0.039 0.777 0.184
 I   E  0.085 0.596 0.319
 P   C  0.093 0.135 0.772
 K   C  0.093 0.164 0.742
 Y   C  0.120 0.132 0.748
 D   C  0.138 0.094 0.768
 N   C  0.162 0.064 0.774
 R   C  0.216 0.139 0.645
 Y   C  0.230 0.204 0.566
 F   C  0.242 0.301 0.457
 G   C  0.255 0.325 0.420
 S   H  0.304 0.393 0.303
 I   H  0.590 0.243 0.167
 A   H  0.818 0.080 0.102
 E   H  0.821 0.052 0.127
 R   H  0.879 0.026 0.096
 F   H  0.934 0.013 0.054
 E   H  0.953 0.011 0.036
 E   H  0.962 0.007 0.032
 M   H  0.965 0.002 0.032
 A   H  0.949 0.010 0.041
 R   H  0.948 0.005 0.048
 E   H  0.887 0.018 0.095
 R   H  0.442 0.155 0.403
 G   C  0.104 0.200 0.696
 L   C  0.151 0.335 0.514
 L   C  0.114 0.450 0.436
 P   C  0.149 0.329 0.522
 I   E  0.166 0.559 0.274
 I   E  0.145 0.577 0.279
 T   C  0.174 0.405 0.420
 C   C  0.181 0.147 0.673
 T   C  0.206 0.124 0.671
 R   C  0.235 0.049 0.716
 R   C  0.131 0.074 0.795
 R   C  0.042 0.039 0.919
 P   C  0.293 0.010 0.697
 E   H  0.544 0.016 0.440
 L   H  0.591 0.087 0.322
 E   H  0.732 0.057 0.211
 I   H  0.877 0.064 0.058
 E   H  0.697 0.235 0.067
 A   H  0.795 0.123 0.082
 V   H  0.790 0.136 0.074
 K   H  0.857 0.052 0.091
 A   H  0.654 0.215 0.131
 M   H  0.481 0.377 0.143
 L   H  0.511 0.251 0.238
 S   H  0.502 0.189 0.309
 W   H  0.539 0.182 0.279
 Q   C  0.360 0.207 0.432
 V   E  0.399 0.419 0.182
 D   E  0.177 0.664 0.159
 W   E  0.226 0.622 0.152
 V   E  0.090 0.866 0.045
 V   E  0.135 0.785 0.080
 A   E  0.245 0.560 0.195
 T   C  0.155 0.228 0.617
 G   C  0.089 0.157 0.754
 A   C  0.053 0.078 0.869
 T   C  0.044 0.065 0.891
 N   C  0.025 0.051 0.924
 P   C  0.164 0.043 0.793
 D   C  0.305 0.028 0.666
 K   H  0.486 0.072 0.442
 I   H  0.621 0.168 0.211
 S   H  0.646 0.186 0.168
 A   H  0.606 0.216 0.177
 L   H  0.427 0.327 0.246
 C   C  0.350 0.242 0.409
 Q   C  0.360 0.124 0.516
 Q   C  0.278 0.127 0.595
 A   C  0.072 0.096 0.832
 G   C  0.021 0.079 0.901
 V   C  0.031 0.207 0.762
 P   C  0.036 0.316 0.648
 T   E  0.041 0.557 0.401
 V   E  0.059 0.475 0.466
 N   C  0.067 0.448 0.486
 L   C  0.060 0.430 0.510
 D   C  0.041 0.349 0.610
 L   C  0.033 0.163 0.804
 P   C  0.033 0.054 0.912
 G   C  0.028 0.068 0.904
 S   C  0.016 0.080 0.904
 L   C  0.024 0.129 0.847
 S   C  0.031 0.149 0.819
 P   C  0.099 0.141 0.760
 S   E  0.088 0.478 0.434
 V   E  0.111 0.613 0.276
 I   E  0.157 0.646 0.198
 S   E  0.253 0.434 0.313
 D   C  0.249 0.220 0.532
 N   C  0.261 0.125 0.614
 Y   C  0.269 0.141 0.590
 G   C  0.232 0.093 0.675
 G   C  0.287 0.049 0.664
 A   C  0.401 0.063 0.536
 K   H  0.558 0.081 0.361
 A   H  0.660 0.167 0.174
 L   H  0.597 0.227 0.177
 T   H  0.579 0.276 0.145
 H   H  0.756 0.142 0.103
 K   H  0.775 0.134 0.091
 I   H  0.764 0.130 0.106
 L   H  0.716 0.177 0.107
 A   H  0.735 0.118 0.147
 N   H  0.732 0.041 0.227
 S   H  0.703 0.023 0.274
 A   H  0.704 0.025 0.271
 R   H  0.696 0.028 0.277
 R   H  0.639 0.050 0.312
 R   H  0.551 0.060 0.389
 G   C  0.371 0.078 0.551
 E   C  0.248 0.167 0.586
 L   C  0.224 0.313 0.463
 A   C  0.174 0.233 0.593
 P   C  0.295 0.137 0.568
 L   C  0.358 0.259 0.383
 T   E  0.316 0.408 0.276
 F   E  0.371 0.388 0.241
 I   C  0.256 0.312 0.432
 G   C  0.170 0.185 0.645
 G   C  0.128 0.114 0.758
 R   C  0.115 0.237 0.648
 R   C  0.157 0.383 0.460
 A   C  0.117 0.356 0.526
 T   E  0.106 0.463 0.430
 I   E  0.140 0.442 0.417
 T   C  0.050 0.328 0.622
 P   C  0.192 0.195 0.613
 A   C  0.193 0.188 0.619
 S   C  0.273 0.242 0.484
 V   H  0.452 0.257 0.291
 Y   H  0.580 0.153 0.267
 A   H  0.439 0.224 0.337
 A   H  0.443 0.172 0.385
 S   C  0.394 0.168 0.439
 T   H  0.471 0.273 0.257
 M   H  0.531 0.289 0.180
 R   H  0.108 0.818 0.074
 I   H  0.305 0.623 0.072
 A   H  0.420 0.451 0.129
 S   H  0.484 0.233 0.283
 W   H  0.640 0.086 0.274
 G   C  0.407 0.114 0.479
 L   E  0.176 0.626 0.198
 A   E  0.307 0.435 0.258
 C   E  0.409 0.200 0.391
 R   C  0.299 0.247 0.454
 R   C  0.351 0.181 0.468
 R   C  0.330 0.183 0.487
 I   E  0.155 0.494 0.351
 F   E  0.362 0.317 0.321
 W   C  0.269 0.194 0.537
 L   C  0.108 0.318 0.574
 P   C  0.273 0.103 0.623
 A   C  0.474 0.225 0.301
 I   C  0.465 0.132 0.403
 R   C  0.148 0.430 0.421
 K   C  0.384 0.189 0.427
 A   H  0.314 0.415 0.270
 T   H  0.251 0.454 0.295
 L   H  0.495 0.319 0.186
 R   H  0.522 0.285 0.193
 T   H  0.720 0.134 0.146
 A   H  0.737 0.111 0.152
 C   H  0.682 0.064 0.253
 R   H  0.766 0.042 0.192
 S   H  0.490 0.137 0.373
 G   C  0.197 0.337 0.467
 L   C  0.498 0.110 0.393
 A   C  0.523 0.105 0.372
 A   C  0.414 0.130 0.456
 R   C  0.397 0.095 0.508
 R   C  0.324 0.155 0.521
 R   C  0.496 0.237 0.267
 C   C  0.306 0.366 0.328
 C   C  0.225 0.292 0.483
 R   C  0.184 0.212 0.604
 G   C  0.062 0.294 0.644
 Y   E  0.024 0.701 0.274
 L   E  0.028 0.762 0.211
 L   E  0.023 0.677 0.301
 T   E  0.021 0.588 0.391
 R   C  0.008 0.331 0.660
 R   C  0.023 0.299 0.678
 Y   C  0.030 0.428 0.542
 P   C  0.037 0.257 0.706
 W   C  0.068 0.248 0.684
 K   C  0.039 0.465 0.497
 G   E  0.005 0.801 0.194
 L   E  0.006 0.818 0.175
 C   E  0.006 0.641 0.353
 A   C  0.004 0.388 0.607
 G   C  0.001 0.418 0.582
 C   C  0.001 0.085 0.914
 R   C  0.000 0.128 0.872
 R   C  0.000 0.342 0.658
 W   E  0.000 0.888 0.112
 V   E  0.000 0.984 0.016

gbiowstest-gor4.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 GorIV_Service_client import *

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

# get a port proxy instance
loc = GorIV_ServiceLocator()
port = loc.getGorIVPort()

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

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

###
# get results
req = getResultsGorIVRequest()
req._JobId = jobid
resp = port.getResultsGorIV(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)

GorIV_Service_client.py

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


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

# Locator
class GorIV_ServiceLocator:
    GorIVPort_address = "http://gbio.ibcp.fr:8090/GorIV_Service"
    def getGorIVPortAddress(self):
        return GorIV_ServiceLocator.GorIVPort_address
    def getGorIVPort(self, url=None, **kw):
        return GorIVBindingSOAP(url or GorIV_ServiceLocator.GorIVPort_address, **kw)

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

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

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

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

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

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

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

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

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

class getResultsGorIVResponse:
    def __init__(self, **kw):
        """Keyword parameters:
        SecStructure -- part SecStructure
        Logout -- part Logout
        """
        self._SecStructure =  kw.get("SecStructure")
        self._Logout =  kw.get("Logout")
getResultsGorIVResponse.typecode = Struct(pname=("urn:GorIV_Service","getResultsGorIVResponse"), 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=getResultsGorIVResponse, encoded="urn:GorIV_Service")

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

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

GorIV_Service_client.pyc (binary file)

GorIV_Service_types.py

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

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

Submitted by cblanchet on Thu, 01/15/2009 - 15:45