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comparison WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/clientGenerator/creatorEngineComplex.py @ 0:049760c677de default tip

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Galaxy WSExtensions added successfully
author uga-galaxy-group
date Tue, 05 Jul 2011 19:34:18 -0400
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-1:000000000000 0:049760c677de
1 '''
2 @author Rui Wang
3 @see LICENSE (MIT style license file).
4 '''
5
6 from types import *
7 import copy
8 import ZSI.TC
9 from introspect import *
10 from msHandler import *
11 from paramConverter import *
12
13 __author__="Rui Wang"
14
15 class ClientCreator(Introspector):
16 """all method to introspect module
17 to return operations&inputs
18 and to invoke operation"""
19
20
21
22 def path2Ops(self, modulePath ):
23 '''given module(the service python file generated by wsdl2py) path,
24 return dictionary of operation name: object (functions of class-**SOAP)'''
25 allclass=self.path2Class(modulePath)
26 #locator=''
27 opclass=''
28 for c in allclass.keys():
29 if c[len(c)-4:len(c)]=='SOAP':
30 opclass=c
31
32
33 #class object of which holds all ops
34 opclassOb=allclass[opclass]
35 #list of names of all ops
36 allattr=dir(opclassOb)
37 #print allattr
38 allops={}
39 for opt in allattr:
40 #every operation object
41 optemp=getattr(opclassOb, opt)
42 #whether it's def and not private such as __init__
43 if callable(optemp) and optemp.__name__.startswith('__')==False:
44 allops[optemp.__name__]=optemp
45
46 return allops
47
48 def path2messageClassOb(self, modulePath):
49 '''given module path,
50 return all message class object'''
51
52
53 allclassOb=self.path2Class(modulePath)
54
55 #find all message classes: has 'typecode', type(obtemp)==ClassType
56 allmsOb=[]
57 for c in allclassOb.values():
58 if hasattr(c,'typecode'):
59 allmsOb.append(c)
60 return allmsOb
61
62 def opname2inputClassOb(self, opName, modulePath):
63 '''given operation name, module path,
64 return input class object'''
65
66 allopNames=self.path2Ops(modulePath)
67 if opName not in allopNames:
68 raise NameError, 'Warning: No operation has the given name!!'
69
70 else:
71 #find all message classes: has 'typecode', type(obtemp)==ClassType
72 allmsOb=self.path2messageClassOb(modulePath)
73 #find input message class of given operation: typecode has pname=operation name
74 for ms in allmsOb:
75 pnameOb=getattr(getattr(ms, 'typecode'), 'pname')
76 if opName==str(pnameOb):
77 inputClass=ms
78 break
79
80 return inputClass
81
82 def opname2outputClassOb(self, opName, modulePath):
83 '''given operation name, module path,
84 return output class object'''
85
86 allopNames=self.path2Ops(modulePath)
87 if opName not in allopNames:
88 raise NameError, 'Warning: No operation has the given name!!'
89
90 else:
91 #find all message classes: has 'typecode', type(obtemp)==ClassType
92 allmsOb=self.path2messageClassOb(modulePath)
93
94 #find output message class of given operation: typecode has pname=operation name+'Response'
95 for ms in allmsOb:
96 pnameOb=getattr(getattr(ms, 'typecode'), 'pname')
97 if opName+'Response'==str(pnameOb):
98 outputClass=ms
99 break
100
101 return outputClass
102
103 def opname2outputs(self, opName, modulePath):
104 '''given operation name, module path,
105 return a list of output nemes of the operation in the module'''
106
107 allopNames=self.path2Ops(modulePath)
108 if opName not in allopNames:
109 raise NameError, 'Warning: No operation has the given name!!'
110
111 else:
112 #get input class object
113 outputClass=self.opname2outputClassOb(opName, modulePath)
114 #find input parameters from message class : instrospect an instace
115 msinstance=outputClass()
116
117 parameters={}
118 mshandler=MessageHandler()
119 parameters=mshandler.msParser(msinstance)
120
121 return parameters
122
123 def opname2inputs(self, opName, modulePath):
124 '''given operation name, module path,
125 return a list of all inputs name of the operation in the given module'''
126
127 allopNames=self.path2Ops(modulePath)
128 if opName not in allopNames:
129 raise NameError, 'Warning: No operation has the given name!!'
130 else:
131 #get input class object
132 inputClass=self.opname2inputClassOb(opName, modulePath)
133
134 parameters={}
135 mshandler=MessageHandler()
136 parameters=mshandler.msParser(inputClass()) #mshandler.flatten(inputClass())
137
138 print 'The parametrrs after flattening : ',parameters
139
140 ofwhat=getattr(getattr(inputClass, 'typecode'), 'ofwhat')
141 paramtypes={}
142 i=0
143 for k in parameters.keys():
144 paramtypes[k]=str(ofwhat[i])
145 i=i+1
146 for l in paramtypes.keys():
147 print "paramters",l
148 origPar=paramtypes[l]
149 copyPar=paramtypes[l]
150 #print copyPar#[-23:-1]
151 newPar=origPar.replace(copyPar[-23:-1],'').strip('<>')
152 paramtypes[l]=newPar
153
154
155
156 # print ofwhat
157 ## for p in ofwhat:
158 ## if isinstance(p, ZSI.TC.ComplexType):
159 ## print 'complextype', p
160 ## elif isinstance(p, ZSI.TC.Array) :
161 ## print 'arraytype', p
162 ## elif isinstance(p,ZSI.TC.String):
163 ## print 'String',p
164 ## elif isinstance(p,ZSI.TC.Integer):
165 ## print 'Integer',p
166 ## else:
167 ## parameters[getattr(p, 'aname')]=None
168 ##
169 #print parameters
170 return parameters
171 #return paramtypes
172 #find input parameters from message class : instrospect an instace
173 # msinstance=inputClass()u can
174 ## print dir(msinstance)
175 # parameters=[]
176 # for i in dir(msinstance):
177 ## print i, type(getattr(msinstance, i))
178 # if (type(getattr(msinstance, i)) is NoneType) and i!='__doc__':
179 # parameters.append(i)
180 ## print parameters
181 # return parameters
182
183 def path2service(self, modulePath):
184 '''given module path,
185 return return service instance
186 instead of: dbfetchSrv = WSDBFetchServerLegacyServiceLocator().getWSDBFetchServerLegacy()'''
187
188 allclass=self.path2Class(modulePath)
189
190 locator=''
191 for c in allclass.keys():
192 if c[len(c)-7:len(c)]=='Locator':
193 locator=c
194
195 locatorClassOb=allclass[locator]
196 for obname in dir(locatorClassOb):
197 obtemp=getattr(locatorClassOb, obname)
198 if (type(obtemp) is MethodType)and not obtemp.__name__.endswith('Address'):
199 serverMethod=obtemp
200 break
201 # Create a service interface
202 service=serverMethod(locatorClassOb())
203 return service
204
205 def invokeOp(self, opName, modulePath, inputs):
206 allopNames=self.path2Ops(modulePath)
207 if opName not in allopNames:
208 raise NameError, 'Warning: No operation has the given name!!'
209 else:
210 # Create a service interface
211 serviceInstance=self.path2service(modulePath)
212
213 #get input class object of given opName
214 inputClass=self.opname2inputClassOb(opName, modulePath)
215
216 mshandler=MessageHandler()
217 if len(inputs) != 0:
218 inputClassInstance=mshandler.msAssign(inputClass(), inputs)
219 else:
220 inputClassInstance= inputClass()
221 #get input name list of given opName
222 # inputNames=self.opname2inputs(opName, modulePath)
223
224 #set value for inputs
225 #request._query = 'UNIPROT:ADH1A_HUMAN'
226 #request._format = 'fasta'
227 # #request._style = 'raw'
228 # if inputNames!= None:
229 # for inName in inputs.keys():
230 # if inName not in inputNames:
231 # raise TypeError, 'the input name is wrong!!!!'
232 # #return None
233 # else:
234 # setattr(inputClassInstance, inName, inputs[inName])
235
236
237 #get dictionary of operation name:object(def)
238 opDict=self.path2Ops(modulePath)
239
240 #get operation object(def)
241 opOb=opDict[opName]
242
243 #invoke operation: response = dbfetchSrv.fetchData(request)
244 responseInstance=opOb(serviceInstance, inputClassInstance)
245
246 #get output from outputmessage: result = response._fetchDataReturn
247 resultDict={}
248 resultDict=mshandler.flatten(responseInstance) #mshandler.msParser(responseInstance)
249 flat = nested2flatDict(resultDict)
250 # outputNames=self.opname2outputs(opName, modulePath)
251 # for out in outputNames:
252 # resultDict[out]=getattr(responseInstance, out)
253
254 #return flat#resultDict
255 return responseInstance
256
257 #testing this module
258 if __name__=="__main__":
259 test=ClientCreator()
260
261 #picr web service
262 # print 'all operations of picr: \n', test.path2Ops('picr.AccessionMapperService_client').keys()
263 # print 'inputs of picr \n', test.opname2inputs('getUPIForSequence', 'picr.AccessionMapperService_client')
264 # print 'outputs of picr \n', test.opname2outputs('getUPIForSequence', 'picr.AccessionMapperService_client')
265
266
267 seq = """>Q8E5Q5_STRA3
268 MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI
269 VAQIVQIVFPVIPGGVTTVAGFLIFGPTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLF
270 MDQKTFDKYESKLETSGYEKFFIFCMASPISPADIMVMITGLSNMSIKRFVTIIMITKPI
271 SIIGYSYLWIYGGDILKNFLN"""
272 # inp = {'_content': [{'_type': 'sequence', '_content': 'MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI'}, {'_type': 'sequence', '_content': 'MDQKTFDKYESKLETSGYEKFFIFCMASPISPADIMVMITGLSNMSIKRFVTIIMITKPI'}], '_params': {'_database': 'swissprot', '_email': 'chaitanya@gmail.com', '_program': 'blastp'}}
273 inp = {'_parameters': {'_stype': 'protein', '_sequence': 'MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI','_database':{ '_string' : ['uniprotkb','uniprotkb_swissprot']}, '_program': 'blastp'}, '_email': 'chaitanya@gmail.com'}
274 inputDict={'_params':{ '_program' : 'blastp', '_database' :'swissprot', '_email' :'riververy@yahoo.com', '_async': 1}, '_content':[{'_type':'sequence', '_content':'MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFI'}]}
275 # inputDict = {}
276 inputs ={'_jobId':'wublast-S20110517-051830-0552-49531676-oy','_type':'out'}
277 inp = {}
278 #print test.invokeOp('run', 'wublast.wublast_services', inp)
279 print test.invokeOp('getParameters', 'wublast.wublast_services', inp)
280 #print test.opname2inputs('getResult','wublast.wublast_services')
281 # print 'all operations: \n', test.path2Ops('blast.WSWUBlast_client').keys()
282 # print 'inputs of runWUBlast \n', test.opname2inputs('runWUBlast', 'blast.WSWUBlast_client')
283 # print 'outputs of runWUBlast \n', test.opname2outputs('runWUBlast', 'blast.WSWUBlast_client')
284
285
286 # modul=test.path2Module('ebiDbfetch.WSDBFetchServerLegacyService_services')
287 # print dir(modul)
288 # print 'all operations: \n', test.path2Ops('ebiDbfetch.WSDBFetchServerLegacyService_services').keys()
289 # print 'inputs of fetchData:\n', test.opname2inputs('fetchData', 'ebiDbfetch.WSDBFetchServerLegacyService_services')
290 # print 'all classes:\n', test.path2Class('ebiDbfetch.WSDBFetchServerLegacyService_services').keys()
291 # print 'service instance ob:\n', test.path2service('ebiDbfetch.WSDBFetchServerLegacyService_services')
292 # print 'outputs of fetchData:\n', test.opname2outputs('fetchData', 'ebiDbfetch.WSDBFetchServerLegacyService_services')
293 # inputDict={'_format':'fasta', '_query':'UNIPROT:ADH1A_HUMAN', '_style':'raw'}
294 # print test.invokeOp('fetchData', 'ebiDbfetch.WSDBFetchServerLegacyService_services', inputDict).values()[0]
295
296 # print 'all operations: \n', test.path2Ops('dbfetch.WSDBFetchServerLegacyService_services').keys()
297 # print 'inputs of fetchData:\n', test.opname2inputs('fetchData', 'dbfetch.WSDBFetchServerLegacyService_services')
298 # inputDict={'_format':'fasta', '_query':'UNIPROT:ADH1A_HUMAN', '_style':'raw'}
299 # print test.invokeOp('fetchData', 'dbfetch.WSDBFetchServerLegacyService_services', inputDict).values()[0]
300
301 #dbfetch.WSDBFetchServerLegacyService_client
302 # print 'all operations: \n', test.path2Ops('dbfetch.WSDBFetchServerLegacyService_client').keys()
303 # print 'inputs of fetchData:\n', test.opname2inputs('fetchData', 'dbfetch.WSDBFetchServerLegacyService_client')
304 # inputDict={'_format':'fasta', '_query':'UNIPROT:ADH1A_HUMAN', '_style':'raw'}
305 # print test.invokeOp('fetchData', 'dbfetch.WSDBFetchServerLegacyService_client', inputDict).values()[0]
306
307
308