webservice_toolsuite: WebServiceToolWorkflow/generateClient1.py~ annotate

author	ganjoo
date	Tue, 07 Jun 2011 18:00:50 -0400
parents
children

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

0

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1 import warnings

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2

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3 with warnings.catch_warnings():

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4 warnings.simplefilter("ignore")

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5 import platform

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6

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7 from jpype._jpackage import JPackage

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8 from jpype import *

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9 import os.path

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10 import sys

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11 import string

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12 from edit_tool_conf1 import *

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13

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14 class ClientGenerator1(object):

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15

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16 #instantiate a client for one time invocation of the selected method of a Web service

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17 def __init__(self,url,methodName,resourceName,fileName):

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18 self.methodName = methodName

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19 self.resourceName=resourceName

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20 self.Ofile = fileName

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21 #replace '__tilda__' with '~'

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22 if(url.find('__tilda__')>-1):

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23 ulist = url.split('__tilda__')

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24 url = '~'.join(ulist)

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25 self.url = url

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26

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27 #replace '**' with ' '

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28 def formatString(self,string):

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29 l = string.split(' ')

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30 return '**'.join(l)

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31

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32 #generates a xml describing a client capable of invoking a Web service described

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33 #using a WADL document. Places this xml tool under ./clients/

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34 def wadlClient(self):

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35 ##parse wadl

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36 #javahome = os.environ.get('JAVA_HOME')

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37 #galaxyhome=os.environ.get('GALAXY_HOME')

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38 #classpath= galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/bin'

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39 #jarpath = galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/lib/'

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40 #machine = platform.machine()

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41

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42 #if machine == 'x86_64' :

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43 # print 'a'

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44 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

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45 #elif machine == 'i686' :

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46 # print 'b'

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47 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

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48 #elif machine == 'sun4u' :

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49 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

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50 #else :

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51 # print 'c'

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52 # System.exit("Could not identify machine, please specify path to libjvm.so")

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53

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54

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55 pkg=JPackage('lsdis')

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56 urlToPass=java.net.URL(self.url)

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57 wadlUrl = self.url

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58

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59 webserviceId = self.methodName

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60 resUrl = self.resourceName

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61

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62 urls = []

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63 methods = []

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64 params = []

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65 docs = []

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66

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67 WADLParserDriver=pkg.WADLParserDriver

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68 wPD=WADLParserDriver()

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69 wPD.parse(urlToPass)

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70 urls = wPD.getUrl()

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71 methods = wPD.getCompleteMethodList()

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72

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73 #write into the output file information about the method and Web service to be invoked.

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74 f=open(self.Ofile,'w')

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75 f.write(wadlUrl)

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76 f.write('\n'+ resUrl)

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77 f.write('\n'+webserviceId)

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78

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79

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80 #get parameters for the selected method of the Web service

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81 i=0

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82 for method in methods:

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83 x = str(method.getId())

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84 y = str(urls.get(i))

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85 if x == webserviceId :

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86 f.write('method matched')

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87 if y == resUrl :

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88 f.write('res matched')

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89 params = method.getRequest().getParams()

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90 break

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91 i=i+1

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92

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93 galaxyhome=os.environ.get('GALAXY_HOME')

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94

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95 #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.

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96 #read the count and increment it.

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97 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','r')

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98 clientCountFile.readline()

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99 clientCountStr = clientCountFile.read(1)

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100 clientCount=string.atoi(clientCountStr)

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101 clientCount=clientCount+1

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102 clientCountFile.close()

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103

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104 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','w')

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105

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106 clientCountFile.write('<count> \n')

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107 clientCountFile.write(str(clientCount))

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108 clientCountFile.write('</count> \n')

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109

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110 #include the count in the tool's name and id to uniquely identify it.

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111 clientName = 'client_'+ str(clientCount)

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112

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113 #create a new xml file under ./clients/

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114 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/'+clientName+'.xml','w')

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115 clientXml.seek(0,0)

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116

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117 #write the tool id, name and description

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118 clientXml.write('<tool id="' + clientName+'1" name="' + self.methodName +' ">\n')

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119 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')

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120

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121 #the one-time invocation tool/client for a REST Web service invokes ./clients/client_1.py to invoke the Web service

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122 #write the command tag to specify the arguments passed to this client_1.py

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123 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +resUrl)

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124

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125 j=0

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126

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127 for param in params:

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128 if param.isRequired():

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129 clientXml.write(' '+self.formatString(param.getName()))

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130 clientXml.write(' $param' + str(j))

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131 j=j+1

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132 clientXml.write(' #else #client_1.py'+' $output ' +resUrl)

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133 j=0

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134 for param in params:

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135 if param.isRequired():

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136 clientXml.write(' '+self.formatString(param.getName()))

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137 clientXml.write(' $param' + str(j))

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138 j=j+1

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139

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140 for param in params:

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141 if not param.isRequired():

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142 clientXml.write(' '+self.formatString(param.getName()))

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143 clientXml.write(' $cond_source.param' + str(j))

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144 j=j+1

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145 clientXml.write(' #end if \n</command>\n')

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146

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147 #start writing inputs

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148 clientXml.write(' <inputs>\n')

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149

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150 #create a param for each required parameter described in the WADL. Check if defaults and options are specified in the WADL

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151 j=0

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152 for param in params:

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153 if param.isRequired():

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154 pName = param.getName()

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155 for doc in param.getDocs():

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156 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":

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157 pName = doc.getInnerText()

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158 if param.getOptions().size()==0:

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159 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')

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160 if not param.getDefault1() == None:

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161 clientXml.write('value="'+param.getDefault1()+'" ')

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162 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')

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163 j=j+1

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164 else:

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165 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )

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166 for option in param.getOptions():

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167 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')

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168 if option.getName() == param.getDefault1():

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169 clientXml.write('selected="true"')

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170 clientXml.write('>'+option.getName()+'</option>\n ')

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171 clientXml.write(' </param> \n')

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172 j=j+1

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173

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174 #create a conditional param for each optional parameter described in the WADL.

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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')

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176 clientXml.write('<when value="no"> \n </when>')

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177 clientXml.write('<when value="yes"> \n')

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178 for param in params:

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179 if not param.isRequired():

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180 pName = param.getName()

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181 for doc in param.getDocs():

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182 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":

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183 pName = doc.getInnerText()

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184 if param.getOptions().size()==0:

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185 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')

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186 if not param.getDefault1() == None:

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187 clientXml.write('value="'+param.getDefault1()+'" ')

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188 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')

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189 j=j+1

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190 else:

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191 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )

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192 for option in param.getOptions():

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193 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')

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194 if option.getName() == param.getDefault1():

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195 clientXml.write('selected="true"')

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196 clientXml.write('>'+option.getName()+'</option>\n ')

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197 clientXml.write(' </param> \n')

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198 j=j+1

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199

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200

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201 clientXml.write('</when>\n</conditional>')

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202 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')

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203

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204 #write information about each parameter in the help section

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205 clientXml.write(' <help>\n')

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206

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207 clientXml.write('Replace white space with ** in all parameter values\n')

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208

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209 for param in params:

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210 if param.isRequired():

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211 pName = param.getName()

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212 for doc in param.getDocs():

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213 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":

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214 pName = doc.getInnerText()

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215 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ pName +' type is ' + param.getType()+'\n')

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216

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217 clientXml.write(' </help>\n</tool>')

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218

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219 #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Tools' section.

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220 editor = editToolConfig1()

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221 editor.addTool(clientName)

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222

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223 ##later add help feature

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224

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225 def sawadlClient(self):

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226 ##parse sawadl

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227 javahome = os.environ.get('JAVA_HOME')

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228 galaxyhome=os.environ.get('GALAXY_HOME')

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229 classpath= galaxyhome + '/tools/WebServiceTool/lib/SAWADLParser/bin'

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230 jarpath = galaxyhome + '/tools/WebServiceTool/lib/'

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231 machine = platform.machine()

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232

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233 #if machine == 'x86_64' :

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234 # print 'a'

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235 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

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236 #elif machine == 'i686' :

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237 # print 'b'

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238 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

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239 #elif machine == 'sun4u' :

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240 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

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241 #else :

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242 # print 'c'

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243 # System.exit("Could not identify machine, please specify path to libjvm.so")

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244

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245

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246 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')

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247 pkgModel =JPackage('org.semanticweb.owlapi.model')

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248 pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding')

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249 pkgVocab = JPackage('org.semanticweb.owlapi.vocab')

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250

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251 DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl"

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252

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253 sawadlUrl = self.url

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254

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255 webserviceId = self.methodName

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256 resUrl = self.resourceName

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257

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258 urls = []

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259 methods = []

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260 params = []

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261 annotationSet = []

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262

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263 SAWADLParserDriver=pkg.SAWADLParserDriver

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264 sawPD=SAWADLParserDriver()

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265 sawPD.parse(sawadlUrl)

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266 urls = sawPD.getUrl()

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267 methods = sawPD.getCompleteMethodList()

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268

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269 IRI = pkgModel.IRI

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270 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary

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271 OWLManager = pkgApiBinding.OWLManager

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272 OWLLiteral = pkgModel.OWLLiteral

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273 owlOntManager = OWLManager.createOWLOntologyManager()

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274 ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI))

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275 dataFactory = owlOntManager.getOWLDataFactory()

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276 propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI())

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277

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278 f=open(self.Ofile,'w')

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279 f.write(sawadlUrl)

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280 f.write('\n'+ resUrl)

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diff changeset

281 f.write('\n'+webserviceId)

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282

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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283

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

284 i=0

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diff changeset

285 for method in methods:

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diff changeset

286 x = str(method.getName())

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287 y = str(urls.get(i))

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288 if x == webserviceId :

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289 f.write('method matched')

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290 if y == resUrl :

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291 f.write('res matched')

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292 params = method.getRequest().getParamList()

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293 break

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294 i=i+1

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295

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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296

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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297

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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298

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299 ##generate client's xml

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300 galaxyhome=os.environ.get('GALAXY_HOME')

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301

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302 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','r')

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303 clientCountFile.readline()

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304 clientCountStr = clientCountFile.read(1)

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305 clientCount=string.atoi(clientCountStr)

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306 clientCount=clientCount+1

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307 clientCountFile.close()

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308

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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309 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','w')

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310 clientCountFile.write('<count> \n')

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311 clientCountFile.write(str(clientCount))

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312 clientCountFile.write('</count> \n')

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313

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314 clientName = 'client_'+ str(clientCount)

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315

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316 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/'+clientName+'.xml','w')

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317 clientXml.seek(0,0)

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318

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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319 clientXml.write('<tool id="' + clientName+'1" name="' + self.methodName +'">\n')

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320 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')

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321

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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322

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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323 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +resUrl)

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324 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop

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325

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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326

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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327 j=0

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328 for param in params:

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329 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':

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330 clientXml.write(' '+self.formatString(param.getName())+'\n')

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331 clientXml.write(' $param' + str(j)+'\n')

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332 j=j+1

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333

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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334 clientXml.write(' #else #client_1.py'+' $output ' +resUrl)

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335 j=0

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336 for param in params:

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337 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':

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338 clientXml.write(' '+self.formatString(param.getName()))

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339 clientXml.write(' $param' + str(j))

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340 j=j+1

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341

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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342 for param in params:

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diff changeset

343 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':

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344 clientXml.write(' '+self.formatString(param.getName()))

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345 clientXml.write(' $cond_source.param' + str(j))

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346 j=j+1

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347

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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348 clientXml.write('#end if \n </command>\n')

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349

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350 ##write inputs depending on required or not. if not required den dont display

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351 ##if required- den check default value, and if options exist.Depending on that

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diff changeset

352 ##decide the type of parameter and options

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353 clientXml.write(' <inputs>\n')

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354

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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355 j=0

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356 for param in params:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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357 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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358 f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size()))

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

359 if param.getOptionvalue().size()==0:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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360 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')

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diff changeset

361 if not param.getDefault1() == None:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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362 clientXml.write('value="'+param.getDefault1()+'" ')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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363 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')

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diff changeset

364 j=j+1

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diff changeset

365 else:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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366 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )

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367 for option in param.getOptionvalue():

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368 clientXml.write(' <option value="'+self.formatString(option)+'" ')

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369 if option == param.getDefault1():

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diff changeset

370 clientXml.write('selected="true"')

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371 clientXml.write('>'+option+'</option>\n ')

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diff changeset

372 clientXml.write(' </param> \n')

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diff changeset

373 j=j+1

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374

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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375

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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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')

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diff changeset

377 clientXml.write('<when value="no"> \n </when>')

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diff changeset

378 clientXml.write('<when value="yes"> \n')

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379

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

380 for param in params:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

381 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':

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diff changeset

382 f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size()))

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diff changeset

383 if param.getOptionvalue().size()==0:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

384 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

385 if not param.getDefault1() == None:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

386 clientXml.write('value="'+param.getDefault1()+'" ')

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diff changeset

387 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')

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diff changeset

388 j=j+1

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

389 else:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

390 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )

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diff changeset

391 for option in param.getOptionvalue():

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

392 clientXml.write(' <option value="'+self.formatString(option)+'" ')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

393 if option == param.getDefault1():

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

394 clientXml.write('selected="true"')

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diff changeset

395 clientXml.write('>'+option+'</option>\n ')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

396 clientXml.write(' </param> \n')

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diff changeset

397 j=j+1

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

398

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

399 clientXml.write('</when>\n</conditional>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

400

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

401 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

402

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

403 clientXml.write(' <help>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

404 for param in params:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

405 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

406 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ param.getName() +': type is ' + param.getType())

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

407

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

408 modelRef = sawPD.getCompleteModelReference(param)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

409 if not modelRef is None:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

410 paramClass = dataFactory.getOWLClass(IRI.create(modelRef));

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

411 annotationSet = paramClass.getAnnotations(ontology,propertyComment)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

412 for annotation in annotationSet:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

413 if isinstance(annotation.getValue(),OWLLiteral):

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

414 val = annotation.getValue()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

415 if val.isOWLStringLiteral() and not val.isOWLTypedLiteral():

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

416 print 'val.getLiteral()=' + val.getLiteral()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

417 clientXml.write(', description from ontology is "' + val.getLiteral()+'"')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

418 break

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

419 clientXml.write('\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

420 clientXml.write(' </help>\n</tool>')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

421 editor = editToolConfig1()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

422 editor.addTool(clientName)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

423

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

424 ##later add help feature

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

425

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

426 def wsdlClient(self):

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

427 ##parse wadl

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

428 javahome = os.environ.get('JAVA_HOME')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

429 galaxyhome=os.environ.get('GALAXY_HOME')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

430 classpath= galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/bin'

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

431 jarpath = galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/lib/'

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

432 machine = platform.machine()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

433

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

434 if machine == 'x86_64' :

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

435 print 'a'

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

436 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

437 elif machine == 'i686' :

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

438 print 'b'

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

439 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

440 elif machine == 'sun4u' :

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

441 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

442 else :

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

443 print 'c'

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

444 System.exit("Could not identify machine, please specify path to libjvm.so")

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

445

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

446

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

447 pkg=JPackage('lsdis')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

448 wsdlUrl = self.url

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

449

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

450 webserviceId = self.methodName

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

451 resUrl = self.resourceName

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

452

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

453 urls = []

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

454 methods = []

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

455 params = []

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

456 paramTypes = []

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

457

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

458 WSDLParserDriver =pkg.WSDLParserDriver

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

459 wPD=WSDLParserDriver()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

460 wPD.parse(wsdlUrl)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

461 methods = wPD.getCompleteMethodList()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

462 urls = wPD.getUrl()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

463

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

464 f=open(self.Ofile,'w')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

465 f.write(wsdlUrl)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

466 f.write('\n'+ resUrl)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

467 f.write('\n'+webserviceId)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

468

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

469

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

470 i=0

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

471 for method in methods:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

472 x = str(method.getName().getLocalPart())

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

473 if x == webserviceId :

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

474 wPD.getParameters(x)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

475 f.write('method matched')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

476 paramTypes = wPD.getParamTypeList()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

477 params = wPD.getParamList()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

478 break

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

479 i=i+1

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

480

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

481

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

482

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

483

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

484 ##generate client's xml

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

485 galaxyhome=os.environ.get('GALAXY_HOME')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

486

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

487 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

488 clientCountFile.readline()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

489 clientCountStr = clientCountFile.read(1)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

490 clientCount=string.atoi(clientCountStr)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

491 clientCount=clientCount+1

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

492 clientCountFile.close()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

493

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

494 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

495 clientCountFile.write('<count> \n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

496 clientCountFile.write(str(clientCount))

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

497 clientCountFile.write('</count> \n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

498

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

499

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

500

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

501

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

502 clientName = 'client_'+ str(clientCount)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

503

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

504 clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

505 clientXml.seek(0,0)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

506

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

507 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +'">\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

508 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

509

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

510

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

511 clientXml.write(' <command interpreter="python">\n client_1.py \n'+' $output \n ' +resUrl+'\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

512 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

513

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

514 j=0

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

515 for param in params:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

516 clientXml.write(' '+self.formatString(param)+'\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

517 clientXml.write(' $param' + str(j)+'\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

518 j=j+1

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

519 clientXml.write('</command>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

520

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

521 ##write inputs depending on required or not. if not required den dont display

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

522 ##if required- den check default value, and if options exist.Depending on that

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

523 ##decide the type of parameter and options

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

524 clientXml.write(' <inputs>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

525

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

526 j=0

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

527 for param in params:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

528 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

529 clientXml.write('type="text" label="'+param+'" help="see tip below" />\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

530 j=j+1

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

531

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

532

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

533

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

534 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

535

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

536 clientXml.write(' <help>\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

537

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

538 clientXml.write('** Replace white with ** in all parameter values **\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

539

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

540 j=0

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

541 for param in params:

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

542 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

543

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

544 clientXml.write(' </help>\n</tool>')

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

545 editor = editToolConfig()

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

546 editor.addTool(clientName)

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

547

d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

548 ##later add help feature

Mercurial > repos > ganjoo > webservice_toolsuite

annotate WebServiceToolWorkflow/generateClient1.py~ @ 0:d5cd409b8a18 default tip