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 f.write('in for loop')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	84 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	85 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	86 if x == webserviceId :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	87 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	88 if y == resUrl :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	89 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	90 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	91 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	92 i=i+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	93
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	94 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	95
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	96 #./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	97 #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	98 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	99 clientCountFile.readline()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	100 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	101 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	102 clientCount=clientCount+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	103 clientCountFile.close()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	104
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	105 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	106
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	107 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	108 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	109 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	110
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	111 #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	112 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	113
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	114 #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	115 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	116 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	117
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	118 #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	119 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	120 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	121
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	122 #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	123 #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	124 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	125
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	126 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	127
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	128 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	129 if param.isRequired():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	130 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	131 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	132 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	133 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	134 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	135 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	136 if param.isRequired():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	137 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	138 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	139 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	140
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	141 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	142 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	143 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	144 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	145 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	146 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	147
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	148 #start writing inputs
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	149 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	150
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	151 #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	152 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	153 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	154 if param.isRequired():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	155 pName = param.getName()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	156 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	157 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	158 pName = doc.getInnerText()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	159 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	160 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	161 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	162 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	163 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	164 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	165 else:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	166 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	167 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	168 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	169 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	170 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	171 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	172 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	173 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	174
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	175 #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	176 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Additional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')
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="no"> \n </when>')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	178 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	179 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	180 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	181 pName = param.getName()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	182 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	183 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	184 pName = doc.getInnerText()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	185 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	186 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	187 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	188 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	189 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	190 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	191 else:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	192 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	193 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	194 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	195 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	196 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	197 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	198 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	199 j=j+1
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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	202 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	203 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	204
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	205 #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	206 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	207
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	208 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	209
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	210 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	211 if param.isRequired():
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	212 pName = param.getName()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	213 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	214 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	215 pName = doc.getInnerText()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	216 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	217
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	218 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	219
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	220 #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	221 editor = editToolConfig1()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	222 editor.addTool(clientName)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	223
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	224 ##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	225
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	226 def sawadlClient(self):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	227 ##parse sawadl
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	228 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	229 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	230 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	231 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	232 machine = platform.machine()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	233
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	234 #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	235 # print 'a'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	236 # 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	237 #elif machine == 'i686' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	238 # print 'b'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	239 # 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	240 #elif machine == 'sun4u' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	241 # 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	242 #else :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	243 # print 'c'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	244 # 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	245
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	246
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	247 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	248 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	249 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	250 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	251
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	252 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	253
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	254 sawadlUrl = self.url
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	255
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	256 webserviceId = self.methodName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	257 resUrl = self.resourceName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	258
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	259 urls = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	260 methods = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	261 params = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	262 annotationSet = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	263
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	264 SAWADLParserDriver=pkg.SAWADLParserDriver
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	265 sawPD=SAWADLParserDriver()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	266 sawPD.parse(sawadlUrl)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	267 urls = sawPD.getUrl()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	268 methods = sawPD.getCompleteMethodList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	269
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	270 IRI = pkgModel.IRI
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	271 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	272 OWLManager = pkgApiBinding.OWLManager
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	273 OWLLiteral = pkgModel.OWLLiteral
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	274 owlOntManager = OWLManager.createOWLOntologyManager()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	275 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	276 dataFactory = owlOntManager.getOWLDataFactory()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	277 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	278
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	279 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	280 f.write(sawadlUrl)
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'+ resUrl)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	282 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	283
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	284
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	285 i=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	286 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	287 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	288 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	289 if x == webserviceId :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	290 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	291 if y == resUrl :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	292 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	293 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	294 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	295 i=i+1
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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	300 ##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	301 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	302
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	303 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	304 clientCountFile.readline()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	305 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	306 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	307 clientCount=clientCount+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	308 clientCountFile.close()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	309
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	310 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	311 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	312 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	313 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	314
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	315 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	316
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	317 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	318 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	319
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	320 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	321 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	322
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	323
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	324 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	325 ##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	326
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	327
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	328 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	329 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	330 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	331 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	332 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	333 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	334
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	335 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	336 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	337 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	338 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	339 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	340 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	341 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	342
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	343 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	344 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	345 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	346 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	347 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	348
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	349 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	350
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	351 ##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	352 ##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	353 ##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	354 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	355
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	356 j=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	357 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	358 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	359 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	360 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	361 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	362 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	363 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	364 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	365 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	366 else:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	367 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	368 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	369 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	370 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	371 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	372 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	373 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	374 j=j+1
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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	377 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Display Additional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')
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="no"> \n </when>')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	379 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	380
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	381 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	382 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	383 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	384 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	385 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	386 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	387 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	388 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	389 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	390 else:
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	391 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	392 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	393 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	394 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	395 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	396 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	397 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	398 j=j+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	399
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	400 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	401
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	402 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	403
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	404 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	405 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	406 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	407 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	408
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	409 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	410 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	411 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	412 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	413 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	414 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	415 val = annotation.getValue()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	416 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	417 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	418 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	419 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	420 clientXml.write('\n')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	421 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	422 editor = editToolConfig1()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	423 editor.addTool(clientName)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	424
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	425 ##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	426
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	427 def wsdlClient(self):
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	428 ##parse wadl
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	429 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	430 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	431 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	432 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	433 machine = platform.machine()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	434
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	435 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	436 print 'a'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	437 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	438 elif machine == 'i686' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	439 print 'b'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	440 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	441 elif machine == 'sun4u' :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	442 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	443 else :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	444 print 'c'
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	445 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	446
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	447
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	448 pkg=JPackage('lsdis')
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	449 wsdlUrl = self.url
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	450
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	451 webserviceId = self.methodName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	452 resUrl = self.resourceName
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	453
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	454 urls = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	455 methods = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	456 params = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	457 paramTypes = []
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	458
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	459 WSDLParserDriver =pkg.WSDLParserDriver
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	460 wPD=WSDLParserDriver()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	461 wPD.parse(wsdlUrl)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	462 methods = wPD.getCompleteMethodList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	463 urls = wPD.getUrl()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	464
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	465 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	466 f.write(wsdlUrl)
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'+ resUrl)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	468 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	469
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	470
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	471 i=0
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	472 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	473 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	474 if x == webserviceId :
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	475 wPD.getParameters(x)
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	476 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	477 paramTypes = wPD.getParamTypeList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	478 params = wPD.getParamList()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	479 break
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	480 i=i+1
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
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	485 ##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	486 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	487
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	488 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	489 clientCountFile.readline()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	490 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	491 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	492 clientCount=clientCount+1
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	493 clientCountFile.close()
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	494
e7482c82796e Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	495 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	496 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	497 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	498 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	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 f.write('in for loop')

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84 x = str(method.getId())

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

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86 if x == webserviceId :

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87 f.write('method matched')

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88 if y == resUrl :

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89 f.write('res matched')

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

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91 break

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92 i=i+1

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93

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

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95

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

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97 #read the count and increment it.

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

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99 clientCountFile.readline()

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100 clientCountStr = clientCountFile.read(1)

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101 clientCount=string.atoi(clientCountStr)

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102 clientCount=clientCount+1

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103 clientCountFile.close()

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104

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

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106

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

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108 clientCountFile.write(str(clientCount))

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

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110

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

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112 clientName = 'client_'+ str(clientCount)

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113

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

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

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116 clientXml.seek(0,0)

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117

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118 #write the tool id, name and description

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

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

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121

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122 #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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123 #write the command tag to specify the arguments passed to this client_1.py

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

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125

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126 j=0

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127

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128 for param in params:

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129 if param.isRequired():

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

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

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132 j=j+1

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

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134 j=0

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135 for param in params:

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136 if param.isRequired():

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

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

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139 j=j+1

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140

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141 for param in params:

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142 if not param.isRequired():

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

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

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145 j=j+1

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

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147

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148 #start writing inputs

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

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150

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151 #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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152 j=0

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153 for param in params:

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154 if param.isRequired():

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155 pName = param.getName()

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156 for doc in param.getDocs():

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

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158 pName = doc.getInnerText()

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

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

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

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

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

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164 j=j+1

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165 else:

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

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167 for option in param.getOptions():

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

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

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

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

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

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173 j=j+1

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174

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

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176 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Additional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')

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

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

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179 for param in params:

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180 if not param.isRequired():

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181 pName = param.getName()

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182 for doc in param.getDocs():

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

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184 pName = doc.getInnerText()

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

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

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

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

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

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190 j=j+1

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191 else:

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

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193 for option in param.getOptions():

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

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

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

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

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

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199 j=j+1

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200

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201

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

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

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204

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205 #write information about each parameter in the help section

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

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207

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

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209

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210 for param in params:

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211 if param.isRequired():

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212 pName = param.getName()

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213 for doc in param.getDocs():

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

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215 pName = doc.getInnerText()

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

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217

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

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219

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

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221 editor = editToolConfig1()

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222 editor.addTool(clientName)

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223

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224 ##later add help feature

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225

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226 def sawadlClient(self):

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227 ##parse sawadl

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

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

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

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

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232 machine = platform.machine()

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233

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234 #if machine == 'x86_64' :

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235 # print 'a'

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

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237 #elif machine == 'i686' :

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238 # print 'b'

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

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240 #elif machine == 'sun4u' :

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

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242 #else :

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243 # print 'c'

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

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245

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246

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

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

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

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

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251

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

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253

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254 sawadlUrl = self.url

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255

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256 webserviceId = self.methodName

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257 resUrl = self.resourceName

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258

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259 urls = []

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260 methods = []

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261 params = []

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262 annotationSet = []

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263

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264 SAWADLParserDriver=pkg.SAWADLParserDriver

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265 sawPD=SAWADLParserDriver()

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266 sawPD.parse(sawadlUrl)

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267 urls = sawPD.getUrl()

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268 methods = sawPD.getCompleteMethodList()

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269

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270 IRI = pkgModel.IRI

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271 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary

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272 OWLManager = pkgApiBinding.OWLManager

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273 OWLLiteral = pkgModel.OWLLiteral

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274 owlOntManager = OWLManager.createOWLOntologyManager()

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diff changeset

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

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diff changeset

276 dataFactory = owlOntManager.getOWLDataFactory()

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diff changeset

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

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278

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

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diff changeset

280 f.write(sawadlUrl)

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diff changeset

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

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diff changeset

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

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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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284

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

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diff changeset

285 i=0

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diff changeset

286 for method in methods:

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diff changeset

287 x = str(method.getName())

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

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diff changeset

289 if x == webserviceId :

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

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290 f.write('method matched')

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diff changeset

291 if y == resUrl :

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

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292 f.write('res matched')

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

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294 break

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295 i=i+1

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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

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

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299

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300 ##generate client's xml

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

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302

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

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304 clientCountFile.readline()

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305 clientCountStr = clientCountFile.read(1)

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306 clientCount=string.atoi(clientCountStr)

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307 clientCount=clientCount+1

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308 clientCountFile.close()

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309

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

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

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

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312 clientCountFile.write(str(clientCount))

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

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314

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315 clientName = 'client_'+ str(clientCount)

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316

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

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

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318 clientXml.seek(0,0)

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319

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

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

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

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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

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

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

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diff changeset

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

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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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diff changeset

327

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

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328 j=0

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329 for param in params:

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330 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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331 clientXml.write(' '+self.formatString(param.getName())+'\n')

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diff changeset

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

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333 j=j+1

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diff changeset

334

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

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335 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

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336 j=0

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

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337 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

338 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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339 clientXml.write(' '+self.formatString(param.getName()))

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

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341 j=j+1

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diff changeset

342

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

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343 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

344 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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345 clientXml.write(' '+self.formatString(param.getName()))

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

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347 j=j+1

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348

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

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

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350

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351 ##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

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352 ##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

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diff changeset

353 ##decide the type of parameter and options

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

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355

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

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356 j=0

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diff changeset

357 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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358 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

359 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

360 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

361 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

362 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

363 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

364 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

365 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

366 else:

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

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diff changeset

367 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

368 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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369 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

370 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

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

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diff changeset

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

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diff changeset

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

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diff changeset

374 j=j+1

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diff changeset

375

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

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376

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

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377 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Display Additional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')

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

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diff changeset

378 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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diff changeset

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

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

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diff changeset

380

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

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diff changeset

381 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

382 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

383 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

384 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

385 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

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diff changeset

386 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

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

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diff changeset

388 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

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diff changeset

389 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

390 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

391 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

392 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

393 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

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diff changeset

394 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

395 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

396 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

397 clientXml.write(' </param> \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

398 j=j+1

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

ganjoo

parents:

diff changeset

399

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

ganjoo

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diff changeset

400 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

401

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

ganjoo

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diff changeset

402 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

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diff changeset

403

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

ganjoo

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diff changeset

404 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

405 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

406 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

407 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

408

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 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

410 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

411 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

412 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

413 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

414 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

415 val = annotation.getValue()

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

ganjoo

parents:

diff changeset

416 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

417 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

418 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

419 break

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

ganjoo

parents:

diff changeset

420 clientXml.write('\n')

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

ganjoo

parents:

diff changeset

421 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

422 editor = editToolConfig1()

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

ganjoo

parents:

diff changeset

423 editor.addTool(clientName)

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

ganjoo

parents:

diff changeset

424

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

ganjoo

parents:

diff changeset

425 ##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

426

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

ganjoo

parents:

diff changeset

427 def wsdlClient(self):

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

ganjoo

parents:

diff changeset

428 ##parse wadl

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

ganjoo

parents:

diff changeset

429 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

430 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

431 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

432 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

433 machine = platform.machine()

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

ganjoo

parents:

diff changeset

434

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

ganjoo

parents:

diff changeset

435 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

436 print 'a'

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

ganjoo

parents:

diff changeset

437 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

438 elif machine == 'i686' :

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

ganjoo

parents:

diff changeset

439 print 'b'

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

ganjoo

parents:

diff changeset

440 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

441 elif machine == 'sun4u' :

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

ganjoo

parents:

diff changeset

442 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

443 else :

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

ganjoo

parents:

diff changeset

444 print 'c'

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

ganjoo

parents:

diff changeset

445 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

446

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

ganjoo

parents:

diff changeset

447

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

ganjoo

parents:

diff changeset

448 pkg=JPackage('lsdis')

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

ganjoo

parents:

diff changeset

449 wsdlUrl = self.url

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

ganjoo

parents:

diff changeset

450

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

ganjoo

parents:

diff changeset

451 webserviceId = self.methodName

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

ganjoo

parents:

diff changeset

452 resUrl = self.resourceName

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

ganjoo

parents:

diff changeset

453

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

ganjoo

parents:

diff changeset

454 urls = []

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

ganjoo

parents:

diff changeset

455 methods = []

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

ganjoo

parents:

diff changeset

456 params = []

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

ganjoo

parents:

diff changeset

457 paramTypes = []

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

ganjoo

parents:

diff changeset

458

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

ganjoo

parents:

diff changeset

459 WSDLParserDriver =pkg.WSDLParserDriver

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

ganjoo

parents:

diff changeset

460 wPD=WSDLParserDriver()

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

ganjoo

parents:

diff changeset

461 wPD.parse(wsdlUrl)

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

ganjoo

parents:

diff changeset

462 methods = wPD.getCompleteMethodList()

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

ganjoo

parents:

diff changeset

463 urls = wPD.getUrl()

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

ganjoo

parents:

diff changeset

464

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

ganjoo

parents:

diff changeset

465 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

466 f.write(wsdlUrl)

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'+ resUrl)

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

ganjoo

parents:

diff changeset

468 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

469

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

ganjoo

parents:

diff changeset

470

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

ganjoo

parents:

diff changeset

471 i=0

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

ganjoo

parents:

diff changeset

472 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

473 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

474 if x == webserviceId :

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

ganjoo

parents:

diff changeset

475 wPD.getParameters(x)

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

ganjoo

parents:

diff changeset

476 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

477 paramTypes = wPD.getParamTypeList()

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

ganjoo

parents:

diff changeset

478 params = wPD.getParamList()

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

ganjoo

parents:

diff changeset

479 break

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

ganjoo

parents:

diff changeset

480 i=i+1

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

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

ganjoo

parents:

diff changeset

485 ##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

486 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

487

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

ganjoo

parents:

diff changeset

488 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

489 clientCountFile.readline()

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

ganjoo

parents:

diff changeset

490 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

491 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

492 clientCount=clientCount+1

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

ganjoo

parents:

diff changeset

493 clientCountFile.close()

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

ganjoo

parents:

diff changeset

494

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

ganjoo

parents:

diff changeset

495 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

496 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

497 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

498 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

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

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

ganjoo

parents:

diff changeset

503 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

504

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

ganjoo

parents:

diff changeset

505 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

506 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

507

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

ganjoo

parents:

diff changeset

508 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

509 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

510

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

ganjoo

parents:

diff changeset

511

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

ganjoo

parents:

diff changeset

512 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

513 ##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

514

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

ganjoo

parents:

diff changeset

515 j=0

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

ganjoo

parents:

diff changeset

516 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

517 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

518 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

519 j=j+1

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

ganjoo

parents:

diff changeset

520 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

521

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

ganjoo

parents:

diff changeset

522 ##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

523 ##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

524 ##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

525 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

526

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

ganjoo

parents:

diff changeset

527 j=0

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

ganjoo

parents:

diff changeset

528 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

529 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

530 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

531 j=j+1

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

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

ganjoo

parents:

diff changeset

535 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

536

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

ganjoo

parents:

diff changeset

537 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

538

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

ganjoo

parents:

diff changeset

539 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

540

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

ganjoo

parents:

diff changeset

541 j=0

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

ganjoo

parents:

diff changeset

542 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

543 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

544

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

ganjoo

parents:

diff changeset

545 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

546 editor = editToolConfig()

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

ganjoo

parents:

diff changeset

547 editor.addTool(clientName)

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

ganjoo

parents:

diff changeset

548

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

ganjoo

parents:

diff changeset

549 ##later add help feature

Mercurial > repos > ganjoo > webservice_toolsuite

annotate WebServiceToolWorkflow/generateClient1.py @ 0:e7482c82796e default tip