webservice_toolsuite: WebServiceToolWorkflow/generateClient1.py~ annotate

author	ganjoo
date	Tue, 07 Jun 2011 17:34:26 -0400
parents
children

rev	line source
0 e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	1 import warnings
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	2
e7482c82796e 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():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	4 warnings.simplefilter("ignore")
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	5 import platform
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	6
e7482c82796e 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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	8 from jpype import *
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	9 import os.path
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	10 import sys
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	11 import string
e7482c82796e 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 *
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	13
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	14 class ClientGenerator1(object):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	15
e7482c82796e 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
e7482c82796e 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):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	18 self.methodName = methodName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	19 self.resourceName=resourceName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	20 self.Ofile = fileName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	21 #replace '__tilda__' with '~'
e7482c82796e 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):
e7482c82796e 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__')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	24 url = '~'.join(ulist)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	25 self.url = url
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	26
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	27 #replace '**' with ' '
e7482c82796e 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):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	29 l = string.split(' ')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	30 return '**'.join(l)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	31
e7482c82796e 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
e7482c82796e 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/
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	34 def wadlClient(self):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	35 ##parse wadl
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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'
e7482c82796e 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/'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	40 #machine = platform.machine()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	41
e7482c82796e 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' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	43 # print 'a'
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	45 #elif machine == 'i686' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	46 # print 'b'
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	48 #elif machine == 'sun4u' :
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	50 #else :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	51 # print 'c'
e7482c82796e 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")
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	53
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	54
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	55 pkg=JPackage('lsdis')
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	57 wadlUrl = self.url
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	58
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	59 webserviceId = self.methodName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	60 resUrl = self.resourceName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	61
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	62 urls = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	63 methods = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	64 params = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	65 docs = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	66
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	67 WADLParserDriver=pkg.WADLParserDriver
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	68 wPD=WADLParserDriver()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	69 wPD.parse(urlToPass)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	70 urls = wPD.getUrl()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	71 methods = wPD.getCompleteMethodList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	72
e7482c82796e 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.
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	75 f.write(wadlUrl)
e7482c82796e 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)
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	78
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	79
e7482c82796e 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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	81 i=0
e7482c82796e 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:
e7482c82796e 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())
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	85 if x == webserviceId :
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	87 if y == resUrl :
e7482c82796e 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')
e7482c82796e 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()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	90 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	91 i=i+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	92
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	94
e7482c82796e 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.
e7482c82796e 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.
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	98 clientCountFile.readline()
e7482c82796e 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)
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	101 clientCount=clientCount+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	102 clientCountFile.close()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	103
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	105
e7482c82796e 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')
e7482c82796e 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))
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	109
e7482c82796e 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.
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	112
e7482c82796e 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/
e7482c82796e 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')
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	116
e7482c82796e 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
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	120
e7482c82796e 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
e7482c82796e 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
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	124
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	125 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	126
e7482c82796e 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:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	128 if param.isRequired():
e7482c82796e 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()))
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	131 j=j+1
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	133 j=0
e7482c82796e 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:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	135 if param.isRequired():
e7482c82796e 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()))
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	138 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	139
e7482c82796e 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:
e7482c82796e 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():
e7482c82796e 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()))
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	144 j=j+1
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	146
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	147 #start writing inputs
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	149
e7482c82796e 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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	151 j=0
e7482c82796e 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:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	153 if param.isRequired():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	154 pName = param.getName()
e7482c82796e 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():
e7482c82796e 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":
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	157 pName = doc.getInnerText()
e7482c82796e 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:
e7482c82796e 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)+'" ')
e7482c82796e 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:
e7482c82796e 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()+'" ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	163 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	164 else:
e7482c82796e 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' )
e7482c82796e 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():
e7482c82796e 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())+'" ')
e7482c82796e 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():
e7482c82796e 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"')
e7482c82796e 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 ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	172 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	173
e7482c82796e 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.
e7482c82796e 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')
e7482c82796e 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>')
e7482c82796e 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')
e7482c82796e 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:
e7482c82796e 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():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	180 pName = param.getName()
e7482c82796e 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():
e7482c82796e 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":
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	183 pName = doc.getInnerText()
e7482c82796e 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:
e7482c82796e 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)+'" ')
e7482c82796e 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:
e7482c82796e 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()+'" ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	189 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	190 else:
e7482c82796e 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' )
e7482c82796e 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():
e7482c82796e 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())+'" ')
e7482c82796e 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():
e7482c82796e 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"')
e7482c82796e 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 ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	198 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	199
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	200
e7482c82796e 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>')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	203
e7482c82796e 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
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	206
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	208
e7482c82796e 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:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	210 if param.isRequired():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	211 pName = param.getName()
e7482c82796e 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():
e7482c82796e 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":
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	214 pName = doc.getInnerText()
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	216
e7482c82796e 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>')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	218
e7482c82796e 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.
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	220 editor = editToolConfig1()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	221 editor.addTool(clientName)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	222
e7482c82796e 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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	224
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	225 def sawadlClient(self):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	226 ##parse sawadl
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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'
e7482c82796e 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/'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	231 machine = platform.machine()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	232
e7482c82796e 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' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	234 # print 'a'
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	236 #elif machine == 'i686' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	237 # print 'b'
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	239 #elif machine == 'sun4u' :
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	241 #else :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	242 # print 'c'
e7482c82796e 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")
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	244
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	245
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	250
e7482c82796e 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"
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	252
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	253 sawadlUrl = self.url
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	254
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	255 webserviceId = self.methodName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	256 resUrl = self.resourceName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	257
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	258 urls = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	259 methods = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	260 params = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	261 annotationSet = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	262
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	263 SAWADLParserDriver=pkg.SAWADLParserDriver
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	264 sawPD=SAWADLParserDriver()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	265 sawPD.parse(sawadlUrl)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	266 urls = sawPD.getUrl()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	267 methods = sawPD.getCompleteMethodList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	268
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	269 IRI = pkgModel.IRI
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	270 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	271 OWLManager = pkgApiBinding.OWLManager
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	272 OWLLiteral = pkgModel.OWLLiteral
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	273 owlOntManager = OWLManager.createOWLOntologyManager()
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	275 dataFactory = owlOntManager.getOWLDataFactory()
e7482c82796e 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())
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	277
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	279 f.write(sawadlUrl)
e7482c82796e 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)
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	282
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	283
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	284 i=0
e7482c82796e 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:
e7482c82796e 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())
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	288 if x == webserviceId :
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	290 if y == resUrl :
e7482c82796e 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')
e7482c82796e 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()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	293 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	294 i=i+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	295
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	296
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	297
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	298
e7482c82796e 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
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	301
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	303 clientCountFile.readline()
e7482c82796e 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)
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	306 clientCount=clientCount+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	307 clientCountFile.close()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	308
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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))
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	313
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	315
e7482c82796e 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')
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	318
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	321
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	322
e7482c82796e 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)
e7482c82796e 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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	325
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	326
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	327 j=0
e7482c82796e 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:
e7482c82796e 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':
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	332 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	333
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	335 j=0
e7482c82796e 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:
e7482c82796e 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':
e7482c82796e 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()))
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	340 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	341
e7482c82796e 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:
e7482c82796e 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':
e7482c82796e 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()))
e7482c82796e 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))
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	346 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	347
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	349
e7482c82796e 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
e7482c82796e 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
e7482c82796e 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
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	354
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	355 j=0
e7482c82796e 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:
e7482c82796e 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':
e7482c82796e 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()))
e7482c82796e 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:
e7482c82796e 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)+'" ')
e7482c82796e 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:
e7482c82796e 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()+'" ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	364 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	365 else:
e7482c82796e 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' )
e7482c82796e 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():
e7482c82796e 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)+'" ')
e7482c82796e 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():
e7482c82796e 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"')
e7482c82796e 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 ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	373 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	374
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	375
e7482c82796e 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')
e7482c82796e 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>')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	379
e7482c82796e 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:
e7482c82796e 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':
e7482c82796e 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()))
e7482c82796e 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:
e7482c82796e 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)+'" ')
e7482c82796e 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:
e7482c82796e 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()+'" ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	388 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	389 else:
e7482c82796e 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' )
e7482c82796e 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():
e7482c82796e 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)+'" ')
e7482c82796e 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():
e7482c82796e 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"')
e7482c82796e 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 ')
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	397 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	398
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	400
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	402
e7482c82796e 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')
e7482c82796e 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:
e7482c82796e 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':
e7482c82796e 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())
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	407
e7482c82796e 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)
e7482c82796e 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:
e7482c82796e 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));
e7482c82796e 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)
e7482c82796e 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:
e7482c82796e 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):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	414 val = annotation.getValue()
e7482c82796e 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():
e7482c82796e 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()
e7482c82796e 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()+'"')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	418 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	419 clientXml.write('\n')
e7482c82796e 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>')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	421 editor = editToolConfig1()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	422 editor.addTool(clientName)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	423
e7482c82796e 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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	425
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	426 def wsdlClient(self):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	427 ##parse wadl
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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'
e7482c82796e 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/'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	432 machine = platform.machine()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	433
e7482c82796e 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' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	435 print 'a'
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	437 elif machine == 'i686' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	438 print 'b'
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	440 elif machine == 'sun4u' :
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	442 else :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	443 print 'c'
e7482c82796e 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")
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	445
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	446
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	447 pkg=JPackage('lsdis')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	448 wsdlUrl = self.url
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	449
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	450 webserviceId = self.methodName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	451 resUrl = self.resourceName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	452
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	453 urls = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	454 methods = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	455 params = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	456 paramTypes = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	457
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	458 WSDLParserDriver =pkg.WSDLParserDriver
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	459 wPD=WSDLParserDriver()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	460 wPD.parse(wsdlUrl)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	461 methods = wPD.getCompleteMethodList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	462 urls = wPD.getUrl()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	463
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	465 f.write(wsdlUrl)
e7482c82796e 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)
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	468
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	469
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	470 i=0
e7482c82796e 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:
e7482c82796e 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())
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	473 if x == webserviceId :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	474 wPD.getParameters(x)
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	476 paramTypes = wPD.getParamTypeList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	477 params = wPD.getParamList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	478 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	479 i=i+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	480
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	481
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	482
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	483
e7482c82796e 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
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	486
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	488 clientCountFile.readline()
e7482c82796e 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)
e7482c82796e 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)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	491 clientCount=clientCount+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	492 clientCountFile.close()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	493
e7482c82796e 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')
e7482c82796e 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')
e7482c82796e 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))
e7482c82796e 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')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	498
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	499
e7482c82796e 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":

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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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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diff changeset

271 OWLManager = pkgApiBinding.OWLManager

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272 OWLLiteral = pkgModel.OWLLiteral

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273 owlOntManager = OWLManager.createOWLOntologyManager()

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diff changeset

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

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275 dataFactory = owlOntManager.getOWLDataFactory()

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diff changeset

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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diff changeset

279 f.write(sawadlUrl)

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diff changeset

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

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diff changeset

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

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282

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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283

e7482c82796e 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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diff changeset

288 if x == webserviceId :

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

289 f.write('method matched')

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diff changeset

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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diff changeset

294 i=i+1

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295

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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296

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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297

e7482c82796e 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

e7482c82796e 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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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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

e7482c82796e 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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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322

e7482c82796e 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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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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326

e7482c82796e 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':

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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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

e7482c82796e 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:

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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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

e7482c82796e 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':

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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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

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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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diff changeset

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

e7482c82796e 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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diff changeset

356 for param in params:

e7482c82796e 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':

e7482c82796e 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()))

e7482c82796e 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:

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

364 j=j+1

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

365 else:

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

367 for option in param.getOptionvalue():

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

369 if option == param.getDefault1():

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

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diff changeset

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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diff changeset

374

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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375

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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

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379

e7482c82796e 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:

e7482c82796e 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':

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e 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)+'" ')

e7482c82796e 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:

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

388 j=j+1

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

389 else:

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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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' )

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

391 for option in param.getOptionvalue():

e7482c82796e 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)+'" ')

e7482c82796e 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():

e7482c82796e 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"')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e 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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

398

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

400

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

402

e7482c82796e 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')

e7482c82796e 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:

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

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

e7482c82796e 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())

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

407

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

408 modelRef = sawPD.getCompleteModelReference(param)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

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diff changeset

409 if not modelRef is None:

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

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diff changeset

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

e7482c82796e 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)

e7482c82796e 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:

e7482c82796e 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):

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

414 val = annotation.getValue()

e7482c82796e 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():

e7482c82796e 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()

e7482c82796e 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()+'"')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

418 break

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

419 clientXml.write('\n')

e7482c82796e 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>')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

421 editor = editToolConfig1()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

422 editor.addTool(clientName)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

423

e7482c82796e 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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

425

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

426 def wsdlClient(self):

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

427 ##parse wadl

e7482c82796e 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')

e7482c82796e 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')

e7482c82796e 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'

e7482c82796e 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/'

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

432 machine = platform.machine()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

433

e7482c82796e 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' :

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

435 print 'a'

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

437 elif machine == 'i686' :

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

438 print 'b'

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

440 elif machine == 'sun4u' :

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

442 else :

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

443 print 'c'

e7482c82796e 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")

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

445

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

446

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

447 pkg=JPackage('lsdis')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

448 wsdlUrl = self.url

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

449

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

450 webserviceId = self.methodName

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

451 resUrl = self.resourceName

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

452

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

453 urls = []

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

454 methods = []

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

455 params = []

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

456 paramTypes = []

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

457

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

458 WSDLParserDriver =pkg.WSDLParserDriver

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

459 wPD=WSDLParserDriver()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

460 wPD.parse(wsdlUrl)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

461 methods = wPD.getCompleteMethodList()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

462 urls = wPD.getUrl()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

463

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

465 f.write(wsdlUrl)

e7482c82796e 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)

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

468

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

469

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

470 i=0

e7482c82796e 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:

e7482c82796e 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())

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

473 if x == webserviceId :

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

474 wPD.getParameters(x)

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

476 paramTypes = wPD.getParamTypeList()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

477 params = wPD.getParamList()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

478 break

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

479 i=i+1

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

480

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

481

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

482

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

483

e7482c82796e 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

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

486

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

488 clientCountFile.readline()

e7482c82796e 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)

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

491 clientCount=clientCount+1

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

492 clientCountFile.close()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

493

e7482c82796e 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')

e7482c82796e 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')

e7482c82796e 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))

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

498

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

499

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

500

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

501

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

503

e7482c82796e 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')

e7482c82796e 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)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

506

e7482c82796e 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')

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

509

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

510

e7482c82796e 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')

e7482c82796e 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

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

513

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

514 j=0

e7482c82796e 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:

e7482c82796e 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')

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

518 j=j+1

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

520

e7482c82796e 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

e7482c82796e 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

e7482c82796e 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

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

525

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

526 j=0

e7482c82796e 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:

e7482c82796e 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)+'" ')

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

530 j=j+1

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

531

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

532

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

533

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

535

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

537

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

539

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

540 j=0

e7482c82796e 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:

e7482c82796e 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')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

543

e7482c82796e 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>')

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

545 editor = editToolConfig()

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

546 editor.addTool(clientName)

e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

ganjoo

parents:

diff changeset

547

e7482c82796e 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:e7482c82796e default tip