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comparison WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient.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 '''
2 @author Chaitanya Guttula, Sumedha Ganjoo
3 @see LICENSE (MIT style license file).
4 '''
5
6 import warnings
7
8 with warnings.catch_warnings():
9 warnings.simplefilter("ignore")
10 import platform
11
12 from jpype._jpackage import JPackage
13 from jpype import *
14 import os.path
15 import sys
16 import string
17 from edit_tool_conf import *
18 from clientGenerator.msHandler import *
19 from clientGenerator.creatorEngineComplex import *
20 from clientGenerator.wsdl2path import *
21 from clientGenerator.paramConverter import *
22
23
24 class ClientGenerator(object):
25
26 #instantiate a client for invocation of the selected method of a Web service in workflows
27 def __init__(self,webservice,operation,outputfile,servicetype):
28 with warnings.catch_warnings():
29 warnings.simplefilter("ignore")
30 self.operation = operation
31 self.webservice = webservice
32 #self.inputs = outputfile
33 self.outputfile = outputfile
34 self.galaxyhome=os.environ.get('GALAXY_HOME')
35 self.clientfile = ''
36 self.servicetype = servicetype
37 if self.servicetype == 'SOAP':
38 wLoad=wsdlLoader()
39 sys.path.append(self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
40 os.chdir(self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
41
42 a = str(self.webservice).split('/')
43 wsdlnamelist = a[len(a)-1].split(".")
44 if len(wsdlnamelist)==1:
45 wsdlnamelist=a[len(a)-1].split('?')
46 print wsdlnamelist
47
48 foldername=wsdlnamelist[0]
49
50 path =self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername
51
52 #creates the client stubs
53 self.clientfile = wLoad.wsdlUrl2path(str(self.webservice),foldername)
54
55 print 'Client file : ',self.clientfile
56 self.paramelement = None
57
58 #replace '__tilda__' with '~'
59 #if(url.find('__tilda__')>-1):
60 # ulist = url.split('__tilda__')
61 #url = '~'.join(ulist)
62 #self.url = url
63
64 '''
65 Checks if a particular paramter is reuired or not. This is used only for soap web services.
66 '''
67 def isRequired(self,param):
68 #j=0
69 #for param in inputl:
70 cc = ClientCreator()
71 self.msinstance = cc.opname2inputClassOb(self.operation,self.clientfile)
72 test = MessageHandler()
73 required = False
74 if (param.find('|$|')>-1):
75 plist = param.split('|')
76 #root = test.getParameter(self.msinstance(),plist[0])
77 k = 0
78 iparam = ''
79 for p in plist:
80 if(k<len(plist)-3):
81 if(k==0):
82 iparam = iparam+(p)
83 else:
84 iparam = iparam+'|'+p
85 k=k+1
86 paramelement = test.getParameter(self.msinstance(),iparam)
87 else:
88 paramelement = test.getParameter(self.msinstance(),param)
89 self.paramelement = paramelement
90 if (param.find('|')>-1):
91 plist = param.split('|')
92 root = test.getParameter(self.msinstance(),plist[0])
93 if not getattr(root,'nillable') and not getattr(paramelement,'nillable'):
94 required = True
95 return True
96 elif getattr(root,'nillable') or (not getattr(root,'nillable') and getattr(paramelement,'nillable')):
97 required = False
98 return False
99 else:
100 if not getattr(paramelement,'nillable'):
101 required = True
102 return True
103 elif getattr(paramelement,'nillable'):
104 required = False
105 return False
106 return required
107
108
109 #replace '**' with ' '
110 def formatString(self,string):
111 l = string.split(' ')
112 return '**'.join(l)
113
114 '''
115 Checks if the tool(operation) is already addded to Galaxy. It opens the tool_conf.xml file and loops through the "Web Service Workflow Tools" sections
116 Then opens each and every tool (xml file) and looks for the description tag for the "Web Service" and "Client for Method" values and then checks
117 if it same as the opearation and web service. As the code is dependent on description of the toool xml file, any change in the description tag
118 of the tool xml file can impact this function.
119 '''
120 def isToolPresent(self):
121
122 f = open(self.galaxyhome+'/tool_conf.xml','r')
123 line = f.readline()
124 linestripped = line.lstrip()
125 linestripped = linestripped.rstrip()
126
127 while linestripped != '<section name="Select Web Service Workflow Tool" id="WebServiceWorkflow">':
128 line = f.readline()
129 linestripped = line.lstrip()
130 linestripped = linestripped.rstrip()
131
132 line = f.readline()
133 linestripped = line.lstrip()
134 linestripped = linestripped.rstrip()
135
136 while linestripped != '</section>':
137 if linestripped.find('<') >-1:
138 toolparts = linestripped.split('"')
139 print '\ntoolparts are : ',toolparts
140 f1 = open(self.galaxyhome+'/tools/'+toolparts[-2],'r')
141 line1 = f1.readline()
142 while not line1.find('<description>') >-1:
143 line1 = f1.readline()
144
145 linestripped1 = line1.lstrip()
146 linestripped1 = linestripped1.rstrip()
147 descriptionparts=linestripped1.split(' ')
148 print '\nOperation : ',descriptionparts
149 service = ''
150 if(self.servicetype == 'SOAP'):
151 service = self.clientfile
152 elif self.servicetype == 'REST':
153 service = self.webservice
154 print 'Service : ',service
155 print 'operation : ',self.operation
156 if(descriptionparts[5]==self.operation and descriptionparts[10] == service):
157 f.close()
158 f1.close()
159 return True
160 f1.close()
161 line = f.readline()
162 linestripped = line.lstrip()
163 linestripped = linestripped.rstrip()
164
165 f.close()
166 return False
167
168
169
170 def wsdlClient(self):
171 with warnings.catch_warnings():
172 warnings.simplefilter("ignore")
173
174 wLoad=wsdlLoader()
175 galaxyhome=os.environ.get('GALAXY_HOME')
176 sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
177 os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
178
179 a = str(self.webservice).split('/')
180 wsdlnamelist = a[len(a)-1].split(".")
181 if len(wsdlnamelist)==1:
182 wsdlnamelist=a[len(a)-1].split('?')
183 print wsdlnamelist
184
185 foldername=wsdlnamelist[0]
186
187 path =galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername
188
189 #creates the client stubs
190 clientfile=wLoad.wsdlUrl2path(str(self.webservice),foldername)
191
192 webservice = clientfile
193 outputfile=open(self.outputfile,'w')
194 test = ClientCreator()
195 print 'inputs of '+self.operation+':\n'
196 inputs= test.opname2inputs(self.operation,webservice)
197 inputl = nested2flatDict(inputs)
198 inputlist = inputl.keys()
199 #noOfInputs=inputlist.count()
200 print '*',inputs,'\n'
201 count =0
202 if (len(inputs)==0):
203 inputs={' ':' '}
204 #inputlist=inputs.keys()
205 for i in inputlist:
206 if count==0:
207 outputfile.write(i+'\t'+webservice+'\t'+self.operation+'\n')
208 else:
209 outputfile.write(i+'\n')
210 count=count+1
211
212 cc = ClientCreator()
213 self.msinstance = cc.opname2inputClassOb(self.operation,webservice)
214 galaxyhome=os.environ.get('GALAXY_HOME')
215
216 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','r')
217 clientCountFile.readline()
218 clientCountStr = clientCountFile.readline()
219
220 clientCount=string.atoi(clientCountStr)
221 clientCount=clientCount+1
222 clientCountFile.close()
223
224 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','w')
225 clientCountFile.write('<count> \n')
226 clientCountFile.write(str(clientCount)+'\n')
227 clientCountFile.write('</count> \n')
228 clientCountFile.close()
229
230
231
232
233 clientName = 'workflowclient_'+ str(clientCount)
234
235 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/'+clientName+'.xml','w')
236 clientXml.seek(0,0)
237
238 clientXml.write('<tool id="' + clientName+'" name="'+foldername+'.' + self.operation +'">\n')
239 clientXml.write(' <description> Client for operation : '+self.operation+' , Web service : '+webservice+' </description>\n')
240
241
242 #clientXml.write(' <command interpreter="python">\n client_1.py \n' +' $output \n ' +self.webservice+' \n '+self.operation+'\n')
243
244 test = MessageHandler()
245
246 #the workflow tool/client for a REST Web service invokes ./workflowclients/client_1.py to invoke the Web service
247 #write the command tag to specify the arguments passed to this client_1.py
248
249 clientXml.write(' <command interpreter="python">\n client_1.py\n'+' #if $cond_source.optional_param_source=="no":\n $output\n $servicetype\n $url\n $method\n' +webservice+ ' '+self.operation+'\n')
250 ##write such that the parameters passed to client_1.py(change name to clientName.py) are dependent on a for loop
251
252 # The paramter having |$| means that it has an elemnet with maxoccurs='unbounded' (i.e. array of strings)
253
254 j=0
255 for param in inputl:
256 if self.isRequired(param):
257 clientXml.write(' "'+param+'"\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
258 j=j+1
259
260 clientXml.write(' #else:\n $output\n $servicetype\n $url\n $method\n' +webservice+' '+self.operation+'\n')
261
262 j=0
263 for param in inputl:
264 if self.isRequired(param):
265 clientXml.write(' "'+param+'"\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
266 j=j+1
267
268 for param in inputl:
269 if not self.isRequired(param):
270 clientXml.write(' "'+param+'"\n #if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user":\n $cond_source.source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $cond_source.source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
271 j=j+1
272
273
274 clientXml.write(' #end if\n')
275
276 clientXml.write('</command>\n')
277
278 #start writing inputs
279 ##write inputs depending on required or not. if not required den dont display
280 ##if required- den check default value, and if options exist.Depending on that
281 ##decide the type of parameter and options
282 ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie
283 clientXml.write(' <inputs>\n')
284 clientXml.write(' <param name="servicetype" type="hidden" value="SOAP" />\n')
285 clientXml.write(' <param name="url" type="hidden" value="'+self.webservice+'" />\n')
286 clientXml.write(' <param name="method" type="hidden" value="'+self.operation+'" />\n')
287
288 j=0
289 for param in inputl:
290 if self.isRequired(param):
291 pName = getattr(self.paramelement,'pname')
292
293 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
294 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
295 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
296 # clientXml.write(' </param> \n')
297 clientXml.write(' </when>\n')
298 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="' + pName + '"/> \n </when>\n </conditional>')
299 j=j+1
300
301
302 clientXml.write(' <conditional name="cond_source">\n <param name="optional_param_source" type="select" label="Display Optional Parameters"> \n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param> \n <when value="no"> \n </when>\n <when value="yes"> \n')
303
304 for param in inputl:
305 if not self.isRequired(param):
306 pName = getattr(self.paramelement,'pname')
307
308 clientXml.write('\n<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n</param>\n <when value="user">')
309 clientXml.write('<param format="text" size = "150" name = "user_param'+str(j)+'" ')
310 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
311 clientXml.write(' </when>\n')
312 clientXml.write('<when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="' + pName + '"/> \n </when>\n </conditional>\n')
313 j=j+1
314
315
316 clientXml.write(' </when>\n </conditional>\n')
317
318 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
319 clientXml.write(' <help>\n')
320 paramtype = None
321 for param in inputl:
322 if self.isRequired(param):
323 if isinstance(self.paramelement,ZSI.TC.String):
324 paramtype = 'String'
325 elif isinstance(self.paramelement,ZSI.TCnumbers.FPfloat):
326 paramtype = 'Floating point'
327 elif isinstance(self.paramelement,ZSI.TC.Boolean):
328 paramtype = 'Boolean'
329 elif isinstance(self.paramelement,ZSI.TCnumbers.Iint):
330 paramtype = 'Integer'
331 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ getattr(self.paramelement,'pname') +': type is ' + paramtype + '\n')
332
333
334 clientXml.write(' </help>\n</tool>')
335
336 # clientXml.write(' <help>\n')
337
338 # j=0
339 # for param in params:
340 # clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')
341
342 # clientXml.write(' </help>\n</tool>')
343 # clientXml.write('</tool>')
344 clientXml.close()
345 editor = editToolConfig()
346 editor.addTool(clientName)
347
348 ##later add help feature
349
350
351
352 def wadlClient(self):
353
354 ##parse wadl
355 pkg=JPackage('lsdis')
356 urlToPass=java.net.URL(self.webservice)
357 wadlUrl = self.webservice
358
359 webserviceId = ''#self.operation
360 resUrl = self.operation
361
362 urls = []
363 methods = []
364 params = []
365
366 #invoke the WADL parser packaged with this tool.
367 WADLParserDriver=pkg.WADLParserDriver
368 wPD=WADLParserDriver()
369 wPD.parse(urlToPass)
370 urls = wPD.getUrl()
371 methods = wPD.getCompleteMethodList()
372
373 a= str(self.webservice).split('/')
374 wadlnamelist = a[len(a)-1].split(".")
375 if len(wadlnamelist)==1:
376 wadlnamelist=a[len(a)-1].split('?')
377 print wadlnamelist
378
379 wadlname=wadlnamelist[0]
380
381 #write into the output file information about the method and Web service to be invoked.
382 f=open(self.outputfile,'w')
383 f.write(self.webservice+'\t')
384 f.write(resUrl+'\t')
385
386 #get parameters for the selected method of the Web service
387 i=0
388 for method in methods:
389 x = str(method.getId())
390 y = str(urls.get(i))
391 webserviceId = x
392 if y == resUrl :
393 params = method.getRequest().getParams()
394 break
395 i=i+1
396
397 f.write(webserviceId)
398
399 galaxyhome=os.environ.get('GALAXY_HOME')
400
401 methodname = resUrl.split('/')
402
403 #./workflowclients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
404 #read the count and increment it.
405 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','r')
406 clientCountFile.readline()
407 clientCountStr = clientCountFile.readline()
408 clientCount=string.atoi(clientCountStr)
409 clientCount=clientCount+1
410 clientCountFile.close()
411
412 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','w')
413 clientCountFile.write('<count> \n')
414 clientCountFile.write(str(clientCount)+'\n')
415 clientCountFile.write('</count> \n')
416
417 #include the count in the tool's name and id to uniquely identify it.
418 clientName = 'workflowclient_'+ str(clientCount)
419
420 #create a new xml file under ./workflowclients/
421 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/'+clientName+'.xml','w')
422 clientXml.seek(0,0)
423
424 #write the tool id, name and description
425 clientXml.write('<tool id="' + clientName+'" name="' + wadlname + '.' + methodname[-1] +'">\n')
426 clientXml.write(' <description> Client for method : '+self.operation+' , Web service : '+self.webservice+' </description>\n')
427
428 #the workflow tool/client for a REST Web service invokes ./workflowclients/client_1.py to invoke the Web service
429 #write the command tag to specify the arguments passed to this client_1.py
430 clientXml.write(' <command interpreter="python">\n client_1.py\n'+' #if $cond_source.optional_param_source=="no":\n $output\n $servicetype\n $url\n $method\n ' +resUrl+'\n')
431
432
433 j=0
434 for param in params:
435 if param.isRequired():
436 clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
437 j=j+1
438
439 clientXml.write(' #else:\n $output\n $servicetype\n $url\n $method\n' +resUrl+'\n')
440 j=0
441 for param in params:
442 if param.isRequired():
443 clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
444 j=j+1
445
446 for param in params:
447 if not param.isRequired():
448 clientXml.write(' '+self.formatString(param.getName())+'\n #if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user":\n $cond_source.source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $cond_source.source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
449 j=j+1
450
451 clientXml.write(' #end if\n')
452 clientXml.write('</command>\n')
453
454 #start writing inputs
455 ##write inputs depending on required or not. if not required den dont display
456 ##if required- den check default value, and if options exist.Depending on that
457 ##decide the type of parameter and options
458 ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie
459
460 clientXml.write(' <inputs>\n')
461 clientXml.write(' <param name="servicetype" type="hidden" value="REST"/>\n')
462 clientXml.write(' <param name="url" type="hidden" value="'+self.webservice+'" />\n')
463 clientXml.write(' <param name="method" type="hidden" value="'+self.operation+'" />\n')
464
465
466 #create a param for each required parameter described in the WADL. Check if defaults are specified. Create param such that
467 #it can either be given a value manually or the value can be taken from a previous step.
468 j=0
469 for param in params:
470 if param.isRequired():
471 pName = param.getName()
472 for doc in param.getDocs():
473 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
474 pName = doc.getInnerText()
475
476 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
477 if param.getOptions().size()==0:
478 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
479 if not param.getDefault1() == None:
480 clientXml.write('value="'+param.getDefault1()+'" ')
481 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
482 else:
483 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
484 for option in param.getOptions():
485 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
486 if option.getName() == param.getDefault1():
487 clientXml.write('selected="true"')
488 clientXml.write('>'+option.getName()+'</option>\n ')
489 clientXml.write(' </param> \n')
490 clientXml.write(' </when>\n')
491 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="' + pName + '"/> \n </when></conditional>')
492 j=j+1
493
494 #create a conditional param for each optional parameter described in the WADL. Again the param can be given a value manually or the value can be taken from
495 #a previous step.
496 clientXml.write(' <conditional name="cond_source">\n <param name="optional_param_source" type="select" label="Display Optional Parameters"> \n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param> \n <when value="no"> \n </when>\n <when value="yes"> \n')
497
498 for param in params:
499 if not param.isRequired():
500 pName = param.getName()
501 for doc in param.getDocs():
502 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
503 pName = doc.getInnerText()
504
505 clientXml.write('\n<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n</param>\n <when value="user">')
506 if param.getOptions().size()==0:
507 clientXml.write('<param format="text" size = "150" name = "user_param'+str(j)+'" ')
508 if not param.getDefault1() == None:
509 clientXml.write('value="'+param.getDefault1()+'" ')
510 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
511 else:
512 clientXml.write('<param name="user_param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
513 for option in param.getOptions():
514 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
515 if option.getName() == param.getDefault1():
516 clientXml.write('selected="true"')
517 clientXml.write('>'+option.getName()+'</option>\n ')
518 clientXml.write(' </param> \n')
519 clientXml.write(' </when>\n')
520 clientXml.write('<when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="' + pName + '"/> \n </when></conditional>\n')
521 j=j+1
522
523
524
525 clientXml.write(' </when>\n </conditional>\n</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
526
527 #write information about each parameter in the help section
528 clientXml.write(' <help>\n')
529 clientXml.write('Replace white space with ** in all parameter values\n')
530
531 for param in params:
532 if param.isRequired():
533 pName = param.getName()
534 for doc in param.getDocs():
535 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
536 pName = doc.getInnerText()
537 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ pName +' type is ' + param.getType()+'\n')
538
539 clientXml.write(' </help>\n</tool>')
540
541 #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Workflow Tools' section.
542 editor = editToolConfig()
543 editor.addTool(clientName)
544
545
546
547
548 def sawadlClient(self):
549 ##parse sawadl
550
551 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
552 pkgModel =JPackage('org.semanticweb.owlapi.model')
553 pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding')
554 pkgVocab = JPackage('org.semanticweb.owlapi.vocab')
555
556 DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl"
557
558 sawadlUrl = self.webservice
559
560 webserviceId = ''#self.inputs
561 resUrl = self.operation
562
563 urls = []
564 methods = []
565 params = []
566 annotationSet = []
567
568 SAWADLParserDriver=pkg.SAWADLParserDriver
569 sawPD=SAWADLParserDriver()
570 sawPD.parse(sawadlUrl)
571 urls = sawPD.getUrl()
572 methods = sawPD.getCompleteMethodList()
573
574 IRI = pkgModel.IRI
575 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
576 OWLManager = pkgApiBinding.OWLManager
577 OWLLiteral = pkgModel.OWLLiteral
578 owlOntManager = OWLManager.createOWLOntologyManager()
579 ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI))
580 dataFactory = owlOntManager.getOWLDataFactory()
581 propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI())
582
583 #write into the output file information about the method and Web service to be invoked.
584 f=open(self.outputfile,'w')
585 f.write(self.webservice+'\t')
586 f.write(resUrl+'\t')
587
588 i=0
589 for method in methods:
590 x = str(method.getName())
591 y = str(urls.get(i))
592 webserviceId = x
593 #if x == webserviceId :
594 if y == resUrl :
595 params = method.getRequest().getParamList()
596 break
597 i=i+1
598
599
600 f.write(webserviceId)
601
602 ##generate client's xml
603 galaxyhome=os.environ.get('GALAXY_HOME')
604
605 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','r')
606 clientCountFile.readline()
607 clientCountStr = clientCountFile.readline()
608 clientCount=string.atoi(clientCountStr)
609 clientCount=clientCount+1
610 clientCountFile.close()
611
612 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','w')
613 clientCountFile.write('<count> \n')
614 clientCountFile.write(str(clientCount)+'\n')
615 clientCountFile.write('</count> \n')
616
617
618
619
620 clientName = 'workflowclient_'+ str(clientCount)
621
622 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/'+clientName+'.xml','w')
623 clientXml.seek(0,0)
624
625 clientXml.write('<tool id="' + clientName+'" name="' + webserviceId +'">\n')
626 clientXml.write(' <description> Client for method: '+webserviceId+' , Web service: '+self.webservice+' </description>\n')
627
628
629 clientXml.write(' <command interpreter="python">\n #client_1.py \n'+' $output \n $servicetype\n $url\n $method\n ' +resUrl+'\n')
630 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
631
632
633 j=0
634 for param in params:
635 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
636 clientXml.write(' '+self.formatString(param.getName())+'\n#if $source'+str(j)+'.source'+str(j)+'_source=="user" $source'+str(j)+'.user_param'+str(j)+' #else $source' + str(j) + '.cached_param' + str(j)+' #end if\n')
637 j=j+1
638 clientXml.write('#if $cond_source.optional_param_source=="yes"')
639
640 for param in params:
641 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
642 clientXml.write(' '+self.formatString(param.getName())+'\n#if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user" $cond_source.source'+str(j)+'.user_param'+str(j)+' #else $cond_source.source' + str(j) + '.cached_param' + str(j)+' #end if\n')
643 j=j+1
644
645 clientXml.write('#else \n#end if\n')
646 clientXml.write('</command>\n')
647
648 ##write inputs depending on required or not. if not required den dont display
649 ##if required- den check default value, and if options exist.Depending on that
650 ##decide the type of parameter and options
651 ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie
652
653 clientXml.write(' <inputs>\n')
654 clientXml.write(' <param name="servicetype" type="hidden" value="REST" />')
655 clientXml.write(' <param name="url" type="hidden" value="'+self.webservice+'" />\n')
656 clientXml.write(' <param name="method" type="hidden" value="'+self.operation+'" />\n')
657
658
659 j=0
660 for param in params:
661 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
662 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
663 if param.getOptionvalue().size()==0:
664 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
665 if not param.getDefault1() == None:
666 clientXml.write('value="'+param.getDefault1()+'" ')
667 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
668 j=j+1
669 else:
670 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
671 for option in param.getOptionvalue():
672 clientXml.write(' <option value="'+self.formatString(option)+'" ')
673 if option == param.getDefault1():
674 clientXml.write('selected="true"')
675 clientXml.write('>'+option+'</option>\n ')
676 clientXml.write(' </param> \n')
677 j=j+1
678 clientXml.write(' </when>\n')
679 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="' + param.getName() + '"/> \n </when></conditional>')
680
681 clientXml.write(' <conditional name="cond_source">\n <param name="optional_param_source" type="select" label="Display Additional Parameters"> \n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param> \n <when value="no"> \n </when>\n <when value="yes"> \n')
682
683 for param in params:
684 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
685 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
686 if param.getOptionvalue().size()==0:
687 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
688 if not param.getDefault1() == None:
689 clientXml.write('value="'+param.getDefault1()+'" ')
690 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
691 j=j+1
692 else:
693 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select'+param.getName()+'" help="see tip below">\n' )
694 for option in param.getOptionvalue():
695 clientXml.write(' <option value="'+self.formatString(option)+'" ')
696 if option == param.getDefault1():
697 clientXml.write('selected="true"')
698 clientXml.write('>'+option+'</option>\n ')
699 clientXml.write(' </param> \n')
700 j=j+1
701 clientXml.write(' </when>\n')
702 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="' + param.getName() + '"/> \n </when></conditional>')
703
704 clientXml.write(' </when>\n </conditional>\n')
705
706 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
707
708 clientXml.write(' <help>\n')
709 for param in params:
710 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
711 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ param.getName() +': type is ' + param.getType())
712
713 modelRef = sawPD.getCompleteModelReference(param)
714 if not modelRef is None:
715 paramClass = dataFactory.getOWLClass(IRI.create(modelRef));
716 annotationSet = paramClass.getAnnotations(ontology,propertyComment)
717 for annotation in annotationSet:
718 if isinstance(annotation.getValue(),OWLLiteral):
719 val = annotation.getValue()
720 if val.isOWLStringLiteral() and not val.isOWLTypedLiteral():
721 print 'val.getLiteral()=' + val.getLiteral()
722 clientXml.write(', description from ontology is "' + val.getLiteral()+'"')
723 break
724 clientXml.write('\n')
725 clientXml.write(' </help>\n</tool>')
726 editor = editToolConfig()
727 editor.addTool(clientName)
728
729
730 def wsdlRestClient(self):
731 ##parse wadl
732 javahome = os.environ.get('JAVA_HOME')
733 galaxyhome=os.environ.get('GALAXY_HOME')
734 classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/bin'
735 jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/lib/'
736 machine = platform.machine()
737
738 if machine == 'x86_64' :
739 print 'a'
740 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
741 elif machine == 'i686' :
742 print 'b'
743 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
744 elif machine == 'sun4u' :
745 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
746 else :
747 print 'c'
748 System.exit("Could not identify machine, please specify path to libjvm.so")
749
750
751 pkg=JPackage('lsdis')
752 wsdlUrl = self.webservice
753
754 webserviceId = ''#self.methodName
755 resUrl = self.operation
756
757 urls = []
758 methods = []
759 params = []
760 paramTypes = []
761
762 WSDLParserDriver =pkg.WSDLParserDriver
763 wPD=WSDLParserDriver()
764 wPD.parse(wsdlUrl)
765 methods = wPD.getCompleteMethodList()
766 urls = wPD.getUrl()
767
768 f=open(self.outputfile,'w')
769 f.write(wsdlUrl+'\t')
770 f.write(resUrl+'\t')
771
772
773 i=0
774 for method in methods:
775 x = str(method.getName().getLocalPart())
776 y = str(url.get(i))
777 webserviceId = x
778 if y == resUrl :
779 wPD.getParameters(x)
780 f.write('method matched')
781 paramTypes = wPD.getParamTypeList()
782 params = wPD.getParamList()
783 break
784 i=i+1
785
786 f.write(webserviceId)
787
788
789
790 ##generate client's xml
791 galaxyhome=os.environ.get('GALAXY_HOME')
792
793 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','r')
794 clientCountFile.readline()
795 clientCountStr = clientCountFile.readline()
796 clientCount=string.atoi(clientCountStr)
797 clientCount=clientCount+1
798 clientCountFile.close()
799
800 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml','w')
801 clientCountFile.write('<count> \n')
802 clientCountFile.write(str(clientCount)+'\n')
803 clientCountFile.write('</count> \n')
804
805
806
807
808 clientName = 'workflowclient_'+ str(clientCount)
809
810 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_RESTSOAP/workflowclients/'+clientName+'.xml','w')
811 clientXml.seek(0,0)
812
813 clientXml.write('<tool id="' + clientName+'" name="' + webserviceId +'">\n')
814 clientXml.write(' <description> Client for method: '+webserviceId+' , Web service: '+self.webservice+' </description>\n')
815
816
817 clientXml.write(' <command interpreter="python">\n client_1.py \n'+' $output \n $servicetype\n $url \n $method' +resUrl+'\n')
818 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
819
820 j=0
821 for param in params:
822 clientXml.write(' '+self.formatString(param)+'\n')
823 clientXml.write(' $param' + str(j)+'\n')
824 j=j+1
825 clientXml.write('</command>\n')
826
827 ##write inputs depending on required or not. if not required den dont display
828 ##if required- den check default value, and if options exist.Depending on that
829 ##decide the type of parameter and options
830 clientXml.write(' <inputs>\n')
831 clientXml.write(' <param name="servicetype" type="hidden" value="REST" />')
832 clientXml.write(' <param name="url" type="hidden" value="'+self.webservice+'" />\n')
833 clientXml.write(' <param name="method" type="hidden" value="'+self.operation+'" />\n')
834
835
836 j=0
837 for param in params:
838 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
839 clientXml.write('type="text" label="'+param+'" help="see tip below" />\n')
840 j=j+1
841
842
843
844 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
845
846 clientXml.write(' <help>\n')
847
848 j=0
849 for param in params:
850 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')
851
852 clientXml.write(' </help>\n</tool>')
853 editor = editToolConfig()
854 editor.addTool(clientName)
855
856 ##later add help feature
857
858 if __name__ == "__main__":
859
860 test = ClientGenerator('http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl','genesbygenetype',None,'REST')
861 present = test.isToolPresent()
862 # required = test.isRequired('_parameters|_sequence')
863 print 'Tool is present : ',present
864