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