Functional test

This is a test of the GOR III protein secondary structure prediction (CNRS IBCP) service.
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Support reference#269-278
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view log 2 weeks agoPASSED

Test began: 2010-08-17 16:57:45 Test ended: 2010-08-17 16:57:54 Result : Test passedDownload this log...
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Test began: 2010-08-15 23:44:53 Test ended: 2010-08-15 23:45:06 Result : Test passedDownload this log...
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Test began: 2010-08-01 11:24:18 Test ended: 2010-08-01 11:24:31 Result : Test passedDownload this log...
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Test began: 2010-08-01 04:20:53 Test ended: 2010-08-01 04:21:08 Result : Test passedDownload this log...
view log 2 months agoPASSED

Test began: 2010-06-28 05:02:30 Test ended: 2010-06-28 05:02:37 Result : Test passedDownload this log...
view log 2 months agoPASSED

Test began: 2010-06-27 07:36:54 Test ended: 2010-06-27 07:37:09 Result : Test passedDownload this log...
view log 3 months agoPASSED

Test began: 2010-06-04 16:42:53 Test ended: 2010-06-04 16:42:58 Result : Test passedDownload this log...
view log 3 months agoFAILED

Test began: 2010-06-02 09:57:48 Test ended: 2010-06-02 09:59:03 Result : Test failure ------ stderr and stdout follow ------ Traceback (most recent call last): File "./gbiowstest-gor3.py", line 63, inDownload this log...resp = port.submitGorIII(req) File "/Library/WebServer.embraceregistry/Documents/sites/all/modules/ws_registry/registry/269/278/package/GorIII_Service_client.py", line 38, in submitGorIII self.binding.Send(None, None, request, soapaction="urn:GorIIIWS.wsdl#submitGorIII", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw) File "build/bdist.macosx-10.5-i386/egg/ZSI/client.py", line 291, in Send File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/httplib.py", line 679, in connect raise socket.error, msg socket.error: (60, 'Operation timed out')
view log 3 months agoFAILED

Test began: 2010-06-01 11:51:13 Test ended: 2010-06-01 11:52:28 Result : Test failure ------ stderr and stdout follow ------ Traceback (most recent call last): File "./gbiowstest-gor3.py", line 63, inDownload this log...resp = port.submitGorIII(req) File "/Library/WebServer.embraceregistry/Documents/sites/all/modules/ws_registry/registry/269/278/package/GorIII_Service_client.py", line 38, in submitGorIII self.binding.Send(None, None, request, soapaction="urn:GorIIIWS.wsdl#submitGorIII", encodingStyle="http://schemas.xmlsoap.org/soap/encoding/", **kw) File "build/bdist.macosx-10.5-i386/egg/ZSI/client.py", line 291, in Send File "/System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/httplib.py", line 679, in connect raise socket.error, msg socket.error: (60, 'Operation timed out')
view log 4 months agoPASSED

Test began: 2010-05-02 23:01:27 Test ended: 2010-05-02 23:01:47 Result : Test passedDownload this log...
This test consists of the following files:
__MACOSX/
._gbiowstest-gor3.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.GorIII
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%
gbiowstest-gor3.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 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)
GorIII_Service_client.py
##################################################
# 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")
GorIII_Service_client.pyc (binary file)
GorIII_Service_types.py
################################################## # 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
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