Functional test

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

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%

#!/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)

##################################################
# 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")

##################################################
# 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