Mercurial > repos > ganjoo > webservice_toolsuite

comparison WebServiceToolWorkflow/generateClient.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_conf import *
13
14 class ClientGenerator(object):
15
16 #instantiate a client for invocation of the selected method of a Web service in workflows
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 ./workflowclients/
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
63 urls = []
64 methods = []
65 params = []
66
67 #invoke the WADL parser packaged with this tool.
68 WADLParserDriver=pkg.WADLParserDriver
69 wPD=WADLParserDriver()
70 wPD.parse(urlToPass)
71 urls = wPD.getUrl()
72 methods = wPD.getCompleteMethodList()
73
74 #write into the output file information about the method and Web service to be invoked.
75 f=open(self.Ofile,'w')
76 f.write(wadlUrl)
77 f.write('\n'+ resUrl)
78 f.write('\n'+webserviceId)
79
80 #get parameters for the selected method of the Web service
81 i=0
82 for method in methods:
83 f.write('\n in methods')
84 x = str(method.getId())
85 y = str(urls.get(i))
86 if x == webserviceId :
87 f.write('\n method matched')
88 f.write('\n y is' + y + ', resUrl is '+resUrl)
89 if y == resUrl :
90 f.write('res matched')
91 params = method.getRequest().getParams()
92 break
93 i=i+1
94
95
96
97 galaxyhome=os.environ.get('GALAXY_HOME')
98
99 #./workflowclients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
100 #read the count and increment it.
101 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/ClientCount.xml','r')
102 clientCountFile.readline()
103 clientCountStr = clientCountFile.read(1)
104 clientCount=string.atoi(clientCountStr)
105 clientCount=clientCount+1
106 clientCountFile.close()
107
108 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/ClientCount.xml','w')
109 clientCountFile.write('<count> \n')
110 clientCountFile.write(str(clientCount))
111 clientCountFile.write('</count> \n')
112
113 #include the count in the tool's name and id to uniquely identify it.
114 clientName = 'client_'+ str(clientCount)
115
116 #create a new xml file under ./workflowclients/
117 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/'+clientName+'.xml','w')
118 clientXml.seek(0,0)
119
120 #write the tool id, name and description
121 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +' ">\n')
122 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
123
124 #the workflow tool/client for a REST Web service invokes ./workflowclients/client_1.py to invoke the Web service
125 #write the command tag to specify the arguments passed to this client_1.py
126 clientXml.write(' <command interpreter="python">\n client_1.py\n'+' #if $cond_source.optional_param_source=="no":\n $output\n ' +resUrl+'\n')
127
128
129 j=0
130 for param in params:
131 if param.isRequired():
132 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')
133 j=j+1
134
135 clientXml.write(' #else:\n $output\n ' +resUrl+'\n')
136 j=0
137 for param in params:
138 if param.isRequired():
139 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')
140 j=j+1
141
142 for param in params:
143 if not param.isRequired():
144 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')
145 j=j+1
146
147 clientXml.write(' #end if\n')
148 clientXml.write('</command>\n')
149
150 #start writing inputs
151 clientXml.write(' <inputs>\n')
152
153 #create a param for each required parameter described in the WADL. Check if defaults are specified. Create param such that
154 #it can either be given a value manually or the value can be taken from a previous step.
155 j=0
156 for param in params:
157 if param.isRequired():
158 pName = param.getName()
159 for doc in param.getDocs():
160 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
161 pName = doc.getInnerText()
162
163 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')
164 if param.getOptions().size()==0:
165 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
166 if not param.getDefault1() == None:
167 clientXml.write('value="'+param.getDefault1()+'" ')
168 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
169 else:
170 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
171 for option in param.getOptions():
172 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
173 if option.getName() == param.getDefault1():
174 clientXml.write('selected="true"')
175 clientXml.write('>'+option.getName()+'</option>\n ')
176 clientXml.write(' </param> \n')
177 clientXml.write(' </when>\n')
178 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>')
179 j=j+1
180
181 #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
182 #a previous step.
183 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')
184
185 for param in params:
186 if not param.isRequired():
187 pName = param.getName()
188 for doc in param.getDocs():
189 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
190 pName = doc.getInnerText()
191
192 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">')
193 if param.getOptions().size()==0:
194 clientXml.write('<param format="text" size = "150" name = "user_param'+str(j)+'" ')
195 if not param.getDefault1() == None:
196 clientXml.write('value="'+param.getDefault1()+'" ')
197 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
198 else:
199 clientXml.write('<param name="user_param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
200 for option in param.getOptions():
201 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
202 if option.getName() == param.getDefault1():
203 clientXml.write('selected="true"')
204 clientXml.write('>'+option.getName()+'</option>\n ')
205 clientXml.write(' </param> \n')
206 clientXml.write(' </when>\n')
207 clientXml.write('<when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>\n')
208 j=j+1
209
210
211
212 clientXml.write(' </when>\n </conditional>\n</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
213
214 #write information about each parameter in the help section
215 clientXml.write(' <help>\n')
216 clientXml.write('Replace white space with ** in all parameter values\n')
217
218 for param in params:
219 if param.isRequired():
220 pName = param.getName()
221 for doc in param.getDocs():
222 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
223 pName = doc.getInnerText()
224 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ pName +' type is ' + param.getType()+'\n')
225
226 clientXml.write(' </help>\n</tool>')
227
228 #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Workflow Tools' section.
229 editor = editToolConfig()
230 editor.addTool(clientName)
231
232
233 def sawadlClient(self):
234 ##parse sawadl
235 javahome = os.environ.get('JAVA_HOME')
236 galaxyhome=os.environ.get('GALAXY_HOME')
237 classpath= galaxyhome + '/tools/WebServiceTool/lib/SAWADLParser/bin'
238 jarpath = galaxyhome + '/tools/WebServiceTool/lib/'
239 machine = platform.machine()
240
241 #if machine == 'x86_64' :
242 # print 'a'
243 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
244 #elif machine == 'i686' :
245 # print 'b'
246 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
247 #elif machine == 'sun4u' :
248 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
249 #else :
250 # print 'c'
251 # System.exit("Could not identify machine, please specify path to libjvm.so")
252
253
254 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
255 pkgModel =JPackage('org.semanticweb.owlapi.model')
256 pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding')
257 pkgVocab = JPackage('org.semanticweb.owlapi.vocab')
258
259 DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl"
260
261 sawadlUrl = self.url
262
263 webserviceId = self.methodName
264 resUrl = self.resourceName
265
266 urls = []
267 methods = []
268 params = []
269 annotationSet = []
270
271 SAWADLParserDriver=pkg.SAWADLParserDriver
272 sawPD=SAWADLParserDriver()
273 sawPD.parse(sawadlUrl)
274 urls = sawPD.getUrl()
275 methods = sawPD.getCompleteMethodList()
276
277 IRI = pkgModel.IRI
278 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
279 OWLManager = pkgApiBinding.OWLManager
280 OWLLiteral = pkgModel.OWLLiteral
281 owlOntManager = OWLManager.createOWLOntologyManager()
282 ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI))
283 dataFactory = owlOntManager.getOWLDataFactory()
284 propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI())
285
286 f=open(self.Ofile,'w')
287 f.write(sawadlUrl)
288 f.write('\n'+ resUrl)
289 f.write('\n'+webserviceId)
290
291
292 i=0
293 for method in methods:
294 x = str(method.getName())
295 y = str(urls.get(i))
296 if x == webserviceId :
297 f.write('method matched')
298 if y == resUrl :
299 f.write('res matched')
300 params = method.getRequest().getParamList()
301 break
302 i=i+1
303
304
305
306
307 ##generate client's xml
308 galaxyhome=os.environ.get('GALAXY_HOME')
309
310 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r')
311 clientCountFile.readline()
312 clientCountStr = clientCountFile.read(1)
313 clientCount=string.atoi(clientCountStr)
314 clientCount=clientCount+1
315 clientCountFile.close()
316
317 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')
318 clientCountFile.write('<count> \n')
319 clientCountFile.write(str(clientCount))
320 clientCountFile.write('</count> \n')
321
322
323
324
325 clientName = 'client_'+ str(clientCount)
326
327 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/'+clientName+'.xml','w')
328 clientXml.seek(0,0)
329
330 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +'">\n')
331 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
332
333
334 clientXml.write(' <command interpreter="python">\n #client_1.py \n'+' $output \n ' +resUrl+'\n')
335 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
336
337
338 j=0
339 for param in params:
340 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
341 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')
342 j=j+1
343 clientXml.write('#if $cond_source.optional_param_source=="yes"')
344
345 for param in params:
346 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
347 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')
348 j=j+1
349
350 clientXml.write('#else \n#end if\n')
351 clientXml.write('</command>\n')
352
353 ##write inputs depending on required or not. if not required den dont display
354 ##if required- den check default value, and if options exist.Depending on that
355 ##decide the type of parameter and options
356 clientXml.write(' <inputs>\n')
357
358
359 j=0
360 for param in params:
361 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
362 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')
363 if param.getOptionvalue().size()==0:
364 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
365 if not param.getDefault1() == None:
366 clientXml.write('value="'+param.getDefault1()+'" ')
367 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
368 j=j+1
369 else:
370 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
371 for option in param.getOptionvalue():
372 clientXml.write(' <option value="'+self.formatString(option)+'" ')
373 if option == param.getDefault1():
374 clientXml.write('selected="true"')
375 clientXml.write('>'+option+'</option>\n ')
376 clientXml.write(' </param> \n')
377 j=j+1
378 clientXml.write(' </when>\n')
379 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>')
380
381 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')
382
383 for param in params:
384 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
385 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')
386 if param.getOptionvalue().size()==0:
387 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
388 if not param.getDefault1() == None:
389 clientXml.write('value="'+param.getDefault1()+'" ')
390 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
391 j=j+1
392 else:
393 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select'+param.getName()+'" help="see tip below">\n' )
394 for option in param.getOptionvalue():
395 clientXml.write(' <option value="'+self.formatString(option)+'" ')
396 if option == param.getDefault1():
397 clientXml.write('selected="true"')
398 clientXml.write('>'+option+'</option>\n ')
399 clientXml.write(' </param> \n')
400 j=j+1
401 clientXml.write(' </when>\n')
402 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>')
403
404 clientXml.write(' </when>\n </conditional>\n')
405
406 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
407
408 clientXml.write(' <help>\n')
409 for param in params:
410 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
411 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ param.getName() +': type is ' + param.getType())
412
413 modelRef = sawPD.getCompleteModelReference(param)
414 if not modelRef is None:
415 paramClass = dataFactory.getOWLClass(IRI.create(modelRef));
416 annotationSet = paramClass.getAnnotations(ontology,propertyComment)
417 for annotation in annotationSet:
418 if isinstance(annotation.getValue(),OWLLiteral):
419 val = annotation.getValue()
420 if val.isOWLStringLiteral() and not val.isOWLTypedLiteral():
421 print 'val.getLiteral()=' + val.getLiteral()
422 clientXml.write(', description from ontology is "' + val.getLiteral()+'"')
423 break
424 clientXml.write('\n')
425 clientXml.write(' </help>\n</tool>')
426 editor = editToolConfig()
427 editor.addTool(clientName)
428
429 ##later add help feature
430
431 def wsdlClient(self):
432 ##parse wadl
433 javahome = os.environ.get('JAVA_HOME')
434 galaxyhome=os.environ.get('GALAXY_HOME')
435 classpath= galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/bin'
436 jarpath = galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/lib/'
437 machine = platform.machine()
438
439 if machine == 'x86_64' :
440 print 'a'
441 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
442 elif machine == 'i686' :
443 print 'b'
444 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
445 elif machine == 'sun4u' :
446 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
447 else :
448 print 'c'
449 System.exit("Could not identify machine, please specify path to libjvm.so")
450
451
452 pkg=JPackage('lsdis')
453 wsdlUrl = self.url
454
455 webserviceId = self.methodName
456 resUrl = self.resourceName
457
458 urls = []
459 methods = []
460 params = []
461 paramTypes = []
462
463 WSDLParserDriver =pkg.WSDLParserDriver
464 wPD=WSDLParserDriver()
465 wPD.parse(wsdlUrl)
466 methods = wPD.getCompleteMethodList()
467 urls = wPD.getUrl()
468
469 f=open(self.Ofile,'w')
470 f.write(wsdlUrl)
471 f.write('\n'+ resUrl)
472 f.write('\n'+webserviceId)
473
474
475 i=0
476 for method in methods:
477 x = str(method.getName().getLocalPart())
478 if x == webserviceId :
479 wPD.getParameters(x)
480 f.write('method matched')
481 paramTypes = wPD.getParamTypeList()
482 params = wPD.getParamList()
483 break
484 i=i+1
485
486
487
488
489 ##generate client's xml
490 galaxyhome=os.environ.get('GALAXY_HOME')
491
492 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r')
493 clientCountFile.readline()
494 clientCountStr = clientCountFile.read(1)
495 clientCount=string.atoi(clientCountStr)
496 clientCount=clientCount+1
497 clientCountFile.close()
498
499 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')
500 clientCountFile.write('<count> \n')
501 clientCountFile.write(str(clientCount))
502 clientCountFile.write('</count> \n')
503
504
505
506
507 clientName = 'client_'+ str(clientCount)
508
509 clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w')
510 clientXml.seek(0,0)
511
512 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +'">\n')
513 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
514
515
516 clientXml.write(' <command interpreter="python">\n client_1.py \n'+' $output \n ' +resUrl+'\n')
517 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
518
519 j=0
520 for param in params:
521 clientXml.write(' '+self.formatString(param)+'\n')
522 clientXml.write(' $param' + str(j)+'\n')
523 j=j+1
524 clientXml.write('</command>\n')
525
526 ##write inputs depending on required or not. if not required den dont display
527 ##if required- den check default value, and if options exist.Depending on that
528 ##decide the type of parameter and options
529 clientXml.write(' <inputs>\n')
530
531 j=0
532 for param in params:
533 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
534 clientXml.write('type="text" label="'+param+'" help="see tip below" />\n')
535 j=j+1
536
537
538
539 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
540
541 clientXml.write(' <help>\n')
542
543 j=0
544 for param in params:
545 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')
546
547 clientXml.write(' </help>\n</tool>')
548 editor = editToolConfig()
549 editor.addTool(clientName)
550
551 ##later add help feature