Mercurial > repos > ganjoo > webservice_toolsuite

comparison WebServiceToolWorkflow/generateClient1.py @ 0:d5cd409b8a18 default tip

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author ganjoo
date Tue, 07 Jun 2011 18:00:50 -0400
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-1:000000000000 0:d5cd409b8a18
1 import warnings
2
3 with warnings.catch_warnings():
4 warnings.simplefilter("ignore")
5 import platform
6
7 from jpype._jpackage import JPackage
8 from jpype import *
9 import os.path
10 import sys
11 import string
12 from edit_tool_conf1 import *
13
14 class ClientGenerator1(object):
15
16 #instantiate a client for one time invocation of the selected method of a Web service
17 def __init__(self,url,methodName,resourceName,fileName):
18 self.methodName = methodName
19 self.resourceName=resourceName
20 self.Ofile = fileName
21 #replace '__tilda__' with '~'
22 if(url.find('__tilda__')>-1):
23 ulist = url.split('__tilda__')
24 url = '~'.join(ulist)
25 self.url = url
26
27 #replace '**' with ' '
28 def formatString(self,string):
29 l = string.split(' ')
30 return '**'.join(l)
31
32 #generates a xml describing a client capable of invoking a Web service described
33 #using a WADL document. Places this xml tool under ./clients/
34 def wadlClient(self):
35 ##parse wadl
36 #javahome = os.environ.get('JAVA_HOME')
37 #galaxyhome=os.environ.get('GALAXY_HOME')
38 #classpath= galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/bin'
39 #jarpath = galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/lib/'
40 #machine = platform.machine()
41
42 #if machine == 'x86_64' :
43 # print 'a'
44 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
45 #elif machine == 'i686' :
46 # print 'b'
47 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
48 #elif machine == 'sun4u' :
49 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
50 #else :
51 # print 'c'
52 # System.exit("Could not identify machine, please specify path to libjvm.so")
53
54
55 pkg=JPackage('lsdis')
56 urlToPass=java.net.URL(self.url)
57 wadlUrl = self.url
58
59 webserviceId = self.methodName
60 resUrl = self.resourceName
61
62 urls = []
63 methods = []
64 params = []
65 docs = []
66
67 WADLParserDriver=pkg.WADLParserDriver
68 wPD=WADLParserDriver()
69 wPD.parse(urlToPass)
70 urls = wPD.getUrl()
71 methods = wPD.getCompleteMethodList()
72
73 #write into the output file information about the method and Web service to be invoked.
74 f=open(self.Ofile,'w')
75 f.write(wadlUrl)
76 f.write('\n'+ resUrl)
77 f.write('\n'+webserviceId)
78
79
80 #get parameters for the selected method of the Web service
81 i=0
82 for method in methods:
83 f.write('in for loop')
84 x = str(method.getId())
85 y = str(urls.get(i))
86 if x == webserviceId :
87 f.write('method matched')
88 if y == resUrl :
89 f.write('res matched')
90 params = method.getRequest().getParams()
91 break
92 i=i+1
93
94 galaxyhome=os.environ.get('GALAXY_HOME')
95
96 #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
97 #read the count and increment it.
98 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','r')
99 clientCountFile.readline()
100 clientCountStr = clientCountFile.read(1)
101 clientCount=string.atoi(clientCountStr)
102 clientCount=clientCount+1
103 clientCountFile.close()
104
105 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','w')
106
107 clientCountFile.write('<count> \n')
108 clientCountFile.write(str(clientCount))
109 clientCountFile.write('</count> \n')
110
111 #include the count in the tool's name and id to uniquely identify it.
112 clientName = 'client_'+ str(clientCount)
113
114 #create a new xml file under ./clients/
115 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/'+clientName+'.xml','w')
116 clientXml.seek(0,0)
117
118 #write the tool id, name and description
119 clientXml.write('<tool id="' + clientName+'1" name="' + self.methodName +' ">\n')
120 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
121
122 #the one-time invocation tool/client for a REST Web service invokes ./clients/client_1.py to invoke the Web service
123 #write the command tag to specify the arguments passed to this client_1.py
124 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +resUrl)
125
126 j=0
127
128 for param in params:
129 if param.isRequired():
130 clientXml.write(' '+self.formatString(param.getName()))
131 clientXml.write(' $param' + str(j))
132 j=j+1
133 clientXml.write(' #else #client_1.py'+' $output ' +resUrl)
134 j=0
135 for param in params:
136 if param.isRequired():
137 clientXml.write(' '+self.formatString(param.getName()))
138 clientXml.write(' $param' + str(j))
139 j=j+1
140
141 for param in params:
142 if not param.isRequired():
143 clientXml.write(' '+self.formatString(param.getName()))
144 clientXml.write(' $cond_source.param' + str(j))
145 j=j+1
146 clientXml.write(' #end if \n</command>\n')
147
148 #start writing inputs
149 clientXml.write(' <inputs>\n')
150
151 #create a param for each required parameter described in the WADL. Check if defaults and options are specified in the WADL
152 j=0
153 for param in params:
154 if param.isRequired():
155 pName = param.getName()
156 for doc in param.getDocs():
157 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
158 pName = doc.getInnerText()
159 if param.getOptions().size()==0:
160 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
161 if not param.getDefault1() == None:
162 clientXml.write('value="'+param.getDefault1()+'" ')
163 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
164 j=j+1
165 else:
166 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
167 for option in param.getOptions():
168 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
169 if option.getName() == param.getDefault1():
170 clientXml.write('selected="true"')
171 clientXml.write('>'+option.getName()+'</option>\n ')
172 clientXml.write(' </param> \n')
173 j=j+1
174
175 #create a conditional param for each optional parameter described in the WADL.
176 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Additional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')
177 clientXml.write('<when value="no"> \n </when>')
178 clientXml.write('<when value="yes"> \n')
179 for param in params:
180 if not param.isRequired():
181 pName = param.getName()
182 for doc in param.getDocs():
183 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
184 pName = doc.getInnerText()
185 if param.getOptions().size()==0:
186 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
187 if not param.getDefault1() == None:
188 clientXml.write('value="'+param.getDefault1()+'" ')
189 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
190 j=j+1
191 else:
192 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
193 for option in param.getOptions():
194 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
195 if option.getName() == param.getDefault1():
196 clientXml.write('selected="true"')
197 clientXml.write('>'+option.getName()+'</option>\n ')
198 clientXml.write(' </param> \n')
199 j=j+1
200
201
202 clientXml.write('</when>\n</conditional>')
203 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
204
205 #write information about each parameter in the help section
206 clientXml.write(' <help>\n')
207
208 clientXml.write('Replace white space with ** in all parameter values\n')
209
210 for param in params:
211 if param.isRequired():
212 pName = param.getName()
213 for doc in param.getDocs():
214 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
215 pName = doc.getInnerText()
216 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ pName +' type is ' + param.getType()+'\n')
217
218 clientXml.write(' </help>\n</tool>')
219
220 #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Tools' section.
221 editor = editToolConfig1()
222 editor.addTool(clientName)
223
224 ##later add help feature
225
226 def sawadlClient(self):
227 ##parse sawadl
228 javahome = os.environ.get('JAVA_HOME')
229 galaxyhome=os.environ.get('GALAXY_HOME')
230 classpath= galaxyhome + '/tools/WebServiceTool/lib/SAWADLParser/bin'
231 jarpath = galaxyhome + '/tools/WebServiceTool/lib/'
232 machine = platform.machine()
233
234 #if machine == 'x86_64' :
235 # print 'a'
236 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
237 #elif machine == 'i686' :
238 # print 'b'
239 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
240 #elif machine == 'sun4u' :
241 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
242 #else :
243 # print 'c'
244 # System.exit("Could not identify machine, please specify path to libjvm.so")
245
246
247 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
248 pkgModel =JPackage('org.semanticweb.owlapi.model')
249 pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding')
250 pkgVocab = JPackage('org.semanticweb.owlapi.vocab')
251
252 DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl"
253
254 sawadlUrl = self.url
255
256 webserviceId = self.methodName
257 resUrl = self.resourceName
258
259 urls = []
260 methods = []
261 params = []
262 annotationSet = []
263
264 SAWADLParserDriver=pkg.SAWADLParserDriver
265 sawPD=SAWADLParserDriver()
266 sawPD.parse(sawadlUrl)
267 urls = sawPD.getUrl()
268 methods = sawPD.getCompleteMethodList()
269
270 IRI = pkgModel.IRI
271 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
272 OWLManager = pkgApiBinding.OWLManager
273 OWLLiteral = pkgModel.OWLLiteral
274 owlOntManager = OWLManager.createOWLOntologyManager()
275 ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI))
276 dataFactory = owlOntManager.getOWLDataFactory()
277 propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI())
278
279 f=open(self.Ofile,'w')
280 f.write(sawadlUrl)
281 f.write('\n'+ resUrl)
282 f.write('\n'+webserviceId)
283
284
285 i=0
286 for method in methods:
287 x = str(method.getName())
288 y = str(urls.get(i))
289 if x == webserviceId :
290 f.write('method matched')
291 if y == resUrl :
292 f.write('res matched')
293 params = method.getRequest().getParamList()
294 break
295 i=i+1
296
297
298
299
300 ##generate client's xml
301 galaxyhome=os.environ.get('GALAXY_HOME')
302
303 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','r')
304 clientCountFile.readline()
305 clientCountStr = clientCountFile.read(1)
306 clientCount=string.atoi(clientCountStr)
307 clientCount=clientCount+1
308 clientCountFile.close()
309
310 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','w')
311 clientCountFile.write('<count> \n')
312 clientCountFile.write(str(clientCount))
313 clientCountFile.write('</count> \n')
314
315 clientName = 'client_'+ str(clientCount)
316
317 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/'+clientName+'.xml','w')
318 clientXml.seek(0,0)
319
320 clientXml.write('<tool id="' + clientName+'1" name="' + self.methodName +'">\n')
321 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
322
323
324 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +resUrl)
325 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
326
327
328 j=0
329 for param in params:
330 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
331 clientXml.write(' '+self.formatString(param.getName())+'\n')
332 clientXml.write(' $param' + str(j)+'\n')
333 j=j+1
334
335 clientXml.write(' #else #client_1.py'+' $output ' +resUrl)
336 j=0
337 for param in params:
338 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
339 clientXml.write(' '+self.formatString(param.getName()))
340 clientXml.write(' $param' + str(j))
341 j=j+1
342
343 for param in params:
344 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
345 clientXml.write(' '+self.formatString(param.getName()))
346 clientXml.write(' $cond_source.param' + str(j))
347 j=j+1
348
349 clientXml.write('#end if \n </command>\n')
350
351 ##write inputs depending on required or not. if not required den dont display
352 ##if required- den check default value, and if options exist.Depending on that
353 ##decide the type of parameter and options
354 clientXml.write(' <inputs>\n')
355
356 j=0
357 for param in params:
358 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
359 f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size()))
360 if param.getOptionvalue().size()==0:
361 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
362 if not param.getDefault1() == None:
363 clientXml.write('value="'+param.getDefault1()+'" ')
364 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
365 j=j+1
366 else:
367 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
368 for option in param.getOptionvalue():
369 clientXml.write(' <option value="'+self.formatString(option)+'" ')
370 if option == param.getDefault1():
371 clientXml.write('selected="true"')
372 clientXml.write('>'+option+'</option>\n ')
373 clientXml.write(' </param> \n')
374 j=j+1
375
376
377 clientXml.write('\n <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')
378 clientXml.write('<when value="no"> \n </when>')
379 clientXml.write('<when value="yes"> \n')
380
381 for param in params:
382 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
383 f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size()))
384 if param.getOptionvalue().size()==0:
385 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
386 if not param.getDefault1() == None:
387 clientXml.write('value="'+param.getDefault1()+'" ')
388 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
389 j=j+1
390 else:
391 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
392 for option in param.getOptionvalue():
393 clientXml.write(' <option value="'+self.formatString(option)+'" ')
394 if option == param.getDefault1():
395 clientXml.write('selected="true"')
396 clientXml.write('>'+option+'</option>\n ')
397 clientXml.write(' </param> \n')
398 j=j+1
399
400 clientXml.write('</when>\n</conditional>\n')
401
402 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
403
404 clientXml.write(' <help>\n')
405 for param in params:
406 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
407 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ param.getName() +': type is ' + param.getType())
408
409 modelRef = sawPD.getCompleteModelReference(param)
410 if not modelRef is None:
411 paramClass = dataFactory.getOWLClass(IRI.create(modelRef));
412 annotationSet = paramClass.getAnnotations(ontology,propertyComment)
413 for annotation in annotationSet:
414 if isinstance(annotation.getValue(),OWLLiteral):
415 val = annotation.getValue()
416 if val.isOWLStringLiteral() and not val.isOWLTypedLiteral():
417 print 'val.getLiteral()=' + val.getLiteral()
418 clientXml.write(', description from ontology is "' + val.getLiteral()+'"')
419 break
420 clientXml.write('\n')
421 clientXml.write(' </help>\n</tool>')
422 editor = editToolConfig1()
423 editor.addTool(clientName)
424
425 ##later add help feature
426
427 def wsdlClient(self):
428 ##parse wadl
429 javahome = os.environ.get('JAVA_HOME')
430 galaxyhome=os.environ.get('GALAXY_HOME')
431 classpath= galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/bin'
432 jarpath = galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/lib/'
433 machine = platform.machine()
434
435 if machine == 'x86_64' :
436 print 'a'
437 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
438 elif machine == 'i686' :
439 print 'b'
440 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
441 elif machine == 'sun4u' :
442 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
443 else :
444 print 'c'
445 System.exit("Could not identify machine, please specify path to libjvm.so")
446
447
448 pkg=JPackage('lsdis')
449 wsdlUrl = self.url
450
451 webserviceId = self.methodName
452 resUrl = self.resourceName
453
454 urls = []
455 methods = []
456 params = []
457 paramTypes = []
458
459 WSDLParserDriver =pkg.WSDLParserDriver
460 wPD=WSDLParserDriver()
461 wPD.parse(wsdlUrl)
462 methods = wPD.getCompleteMethodList()
463 urls = wPD.getUrl()
464
465 f=open(self.Ofile,'w')
466 f.write(wsdlUrl)
467 f.write('\n'+ resUrl)
468 f.write('\n'+webserviceId)
469
470
471 i=0
472 for method in methods:
473 x = str(method.getName().getLocalPart())
474 if x == webserviceId :
475 wPD.getParameters(x)
476 f.write('method matched')
477 paramTypes = wPD.getParamTypeList()
478 params = wPD.getParamList()
479 break
480 i=i+1
481
482
483
484
485 ##generate client's xml
486 galaxyhome=os.environ.get('GALAXY_HOME')
487
488 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r')
489 clientCountFile.readline()
490 clientCountStr = clientCountFile.read(1)
491 clientCount=string.atoi(clientCountStr)
492 clientCount=clientCount+1
493 clientCountFile.close()
494
495 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')
496 clientCountFile.write('<count> \n')
497 clientCountFile.write(str(clientCount))
498 clientCountFile.write('</count> \n')
499
500
501
502
503 clientName = 'client_'+ str(clientCount)
504
505 clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w')
506 clientXml.seek(0,0)
507
508 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +'">\n')
509 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
510
511
512 clientXml.write(' <command interpreter="python">\n client_1.py \n'+' $output \n ' +resUrl+'\n')
513 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
514
515 j=0
516 for param in params:
517 clientXml.write(' '+self.formatString(param)+'\n')
518 clientXml.write(' $param' + str(j)+'\n')
519 j=j+1
520 clientXml.write('</command>\n')
521
522 ##write inputs depending on required or not. if not required den dont display
523 ##if required- den check default value, and if options exist.Depending on that
524 ##decide the type of parameter and options
525 clientXml.write(' <inputs>\n')
526
527 j=0
528 for param in params:
529 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
530 clientXml.write('type="text" label="'+param+'" help="see tip below" />\n')
531 j=j+1
532
533
534
535 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
536
537 clientXml.write(' <help>\n')
538
539 clientXml.write('** Replace white with ** in all parameter values **\n')
540
541 j=0
542 for param in params:
543 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')
544
545 clientXml.write(' </help>\n</tool>')
546 editor = editToolConfig()
547 editor.addTool(clientName)
548
549 ##later add help feature