webservice_toolsuite: WebServiceToolWorkflow/generateClient.py annotate

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

rev	line source
0 d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	1 import warnings
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	2
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	3 with warnings.catch_warnings():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	4 warnings.simplefilter("ignore")
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	5 import platform
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	6
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	7 from jpype._jpackage import JPackage
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	8 from jpype import *
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	9 import os.path
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	10 import sys
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	11 import string
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	12 from edit_tool_conf import *
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	13
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	14 class ClientGenerator(object):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	15
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	16 #instantiate a client for invocation of the selected method of a Web service in workflows
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	17 def __init__(self,url,methodName,resourceName,fileName):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	18 self.methodName = methodName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	19 self.resourceName=resourceName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	20 self.Ofile = fileName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	21 #replace '__tilda__' with '~'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	22 if(url.find('__tilda__')>-1):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	23 ulist = url.split('__tilda__')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	24 url = '~'.join(ulist)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	25 self.url = url
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	26
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	27 #replace '**' with ' '
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	28 def formatString(self,string):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	29 l = string.split(' ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	30 return '**'.join(l)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	31
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	32 #generates a xml describing a client capable of invoking a Web service described
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	33 #using a WADL document. Places this xml tool under ./workflowclients/
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	34 def wadlClient(self):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	35 ##parse wadl
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	36 #javahome = os.environ.get('JAVA_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	37 #galaxyhome=os.environ.get('GALAXY_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	38 #classpath= galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/bin'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	39 #jarpath = galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/lib/'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	40 #machine = platform.machine()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	41
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	42 #if machine == 'x86_64' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	43 # print 'a'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	44 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	45 #elif machine == 'i686' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	46 # print 'b'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	47 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	48 #elif machine == 'sun4u' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	49 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	50 #else :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	51 # print 'c'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	52 # System.exit("Could not identify machine, please specify path to libjvm.so")
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	53
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	54
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	55 pkg=JPackage('lsdis')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	56 urlToPass=java.net.URL(self.url)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	57 wadlUrl = self.url
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	58
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	59 webserviceId = self.methodName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	60 resUrl = self.resourceName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	61
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	62
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	63 urls = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	64 methods = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	65 params = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	66
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	67 #invoke the WADL parser packaged with this tool.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	68 WADLParserDriver=pkg.WADLParserDriver
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	69 wPD=WADLParserDriver()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	70 wPD.parse(urlToPass)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	71 urls = wPD.getUrl()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	72 methods = wPD.getCompleteMethodList()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	73
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	74 #write into the output file information about the method and Web service to be invoked.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	75 f=open(self.Ofile,'w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	76 f.write(wadlUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	77 f.write('\n'+ resUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	78 f.write('\n'+webserviceId)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	79
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	80 #get parameters for the selected method of the Web service
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	81 i=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	82 for method in methods:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	83 f.write('\n in methods')
d5cd409b8a18 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())
d5cd409b8a18 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))
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	86 if x == webserviceId :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	87 f.write('\n method matched')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	88 f.write('\n y is' + y + ', resUrl is '+resUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	89 if y == resUrl :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	90 f.write('res matched')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	91 params = method.getRequest().getParams()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	92 break
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	93 i=i+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	94
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	95
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	96
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	97 galaxyhome=os.environ.get('GALAXY_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	98
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	99 #./workflowclients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	100 #read the count and increment it.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	101 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/ClientCount.xml','r')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	102 clientCountFile.readline()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	103 clientCountStr = clientCountFile.read(1)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	104 clientCount=string.atoi(clientCountStr)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	105 clientCount=clientCount+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	106 clientCountFile.close()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	107
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	108 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/ClientCount.xml','w')
d5cd409b8a18 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')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	110 clientCountFile.write(str(clientCount))
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	111 clientCountFile.write('</count> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	112
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	113 #include the count in the tool's name and id to uniquely identify it.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	114 clientName = 'client_'+ str(clientCount)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	115
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	116 #create a new xml file under ./workflowclients/
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	117 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/'+clientName+'.xml','w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	118 clientXml.seek(0,0)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	119
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	120 #write the tool id, name and description
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	121 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +' ">\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	122 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	123
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	124 #the workflow tool/client for a REST Web service invokes ./workflowclients/client_1.py to invoke the Web service
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	125 #write the command tag to specify the arguments passed to this client_1.py
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	126 clientXml.write(' <command interpreter="python">\n client_1.py\n'+' #if $cond_source.optional_param_source=="no":\n $output\n ' +resUrl+'\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	127
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	128
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	129 j=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	130 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	131 if param.isRequired():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	132 clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	133 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	134
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	135 clientXml.write(' #else:\n $output\n ' +resUrl+'\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	136 j=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	137 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	138 if param.isRequired():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	139 clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	140 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	141
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	142 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	143 if not param.isRequired():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	144 clientXml.write(' '+self.formatString(param.getName())+'\n #if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user":\n $cond_source.source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $cond_source.source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	145 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	146
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	147 clientXml.write(' #end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	148 clientXml.write('</command>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	149
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	150 #start writing inputs
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	151 clientXml.write(' <inputs>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	152
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	153 #create a param for each required parameter described in the WADL. Check if defaults are specified. Create param such that
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	154 #it can either be given a value manually or the value can be taken from a previous step.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	155 j=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	156 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	157 if param.isRequired():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	158 pName = param.getName()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	159 for doc in param.getDocs():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	160 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	161 pName = doc.getInnerText()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	162
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	163 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	164 if param.getOptions().size()==0:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	165 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	166 if not param.getDefault1() == None:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	167 clientXml.write('value="'+param.getDefault1()+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	168 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	169 else:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	170 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	171 for option in param.getOptions():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	172 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	173 if option.getName() == param.getDefault1():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	174 clientXml.write('selected="true"')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	175 clientXml.write('>'+option.getName()+'</option>\n ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	176 clientXml.write(' </param> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	177 clientXml.write(' </when>\n')
d5cd409b8a18 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="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	179 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	180
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	181 #create a conditional param for each optional parameter described in the WADL. Again the param can be given a value manually or the value can be taken from
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	182 #a previous step.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	183 clientXml.write(' <conditional name="cond_source">\n <param name="optional_param_source" type="select" label="Display Additional Parameters"> \n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param> \n <when value="no"> \n </when>\n <when value="yes"> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	184
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	185 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	186 if not param.isRequired():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	187 pName = param.getName()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	188 for doc in param.getDocs():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	189 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	190 pName = doc.getInnerText()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	191
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	192 clientXml.write('\n<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n</param>\n <when value="user">')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	193 if param.getOptions().size()==0:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	194 clientXml.write('<param format="text" size = "150" name = "user_param'+str(j)+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	195 if not param.getDefault1() == None:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	196 clientXml.write('value="'+param.getDefault1()+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	197 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	198 else:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	199 clientXml.write('<param name="user_param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	200 for option in param.getOptions():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	201 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	202 if option.getName() == param.getDefault1():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	203 clientXml.write('selected="true"')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	204 clientXml.write('>'+option.getName()+'</option>\n ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	205 clientXml.write(' </param> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	206 clientXml.write(' </when>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	207 clientXml.write('<when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	208 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	209
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	210
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	211
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	212 clientXml.write(' </when>\n </conditional>\n</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	213
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	214 #write information about each parameter in the help section
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	215 clientXml.write(' <help>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	216 clientXml.write('Replace white space with ** in all parameter values\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	217
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	218 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	219 if param.isRequired():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	220 pName = param.getName()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	221 for doc in param.getDocs():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	222 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	223 pName = doc.getInnerText()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	224 clientXml.write('\n.. class:: infomark\n\nTIP: '+ pName +' type is ' + param.getType()+'\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	225
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	226 clientXml.write(' </help>\n</tool>')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	227
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	228 #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Workflow Tools' section.
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	229 editor = editToolConfig()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	230 editor.addTool(clientName)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	231
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	232
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	233 def sawadlClient(self):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	234 ##parse sawadl
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	235 javahome = os.environ.get('JAVA_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	236 galaxyhome=os.environ.get('GALAXY_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	237 classpath= galaxyhome + '/tools/WebServiceTool/lib/SAWADLParser/bin'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	238 jarpath = galaxyhome + '/tools/WebServiceTool/lib/'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	239 machine = platform.machine()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	240
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	241 #if machine == 'x86_64' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	242 # print 'a'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	243 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	244 #elif machine == 'i686' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	245 # print 'b'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	246 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	247 #elif machine == 'sun4u' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	248 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	249 #else :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	250 # print 'c'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	251 # System.exit("Could not identify machine, please specify path to libjvm.so")
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	252
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	253
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	254 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	255 pkgModel =JPackage('org.semanticweb.owlapi.model')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	256 pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	257 pkgVocab = JPackage('org.semanticweb.owlapi.vocab')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	258
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	259 DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl"
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	260
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	261 sawadlUrl = self.url
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	262
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	263 webserviceId = self.methodName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	264 resUrl = self.resourceName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	265
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	266 urls = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	267 methods = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	268 params = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	269 annotationSet = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	270
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	271 SAWADLParserDriver=pkg.SAWADLParserDriver
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	272 sawPD=SAWADLParserDriver()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	273 sawPD.parse(sawadlUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	274 urls = sawPD.getUrl()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	275 methods = sawPD.getCompleteMethodList()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	276
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	277 IRI = pkgModel.IRI
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	278 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	279 OWLManager = pkgApiBinding.OWLManager
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	280 OWLLiteral = pkgModel.OWLLiteral
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	281 owlOntManager = OWLManager.createOWLOntologyManager()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	282 ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI))
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	283 dataFactory = owlOntManager.getOWLDataFactory()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	284 propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI())
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	285
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	286 f=open(self.Ofile,'w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	287 f.write(sawadlUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	288 f.write('\n'+ resUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	289 f.write('\n'+webserviceId)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	290
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	291
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	292 i=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	293 for method in methods:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	294 x = str(method.getName())
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	295 y = str(urls.get(i))
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	296 if x == webserviceId :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	297 f.write('method matched')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	298 if y == resUrl :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	299 f.write('res matched')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	300 params = method.getRequest().getParamList()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	301 break
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	302 i=i+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	303
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	304
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	305
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	306
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	307 ##generate client's xml
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	308 galaxyhome=os.environ.get('GALAXY_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	309
d5cd409b8a18 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/WebServiceTool/clients/ClientCount.xml','r')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	311 clientCountFile.readline()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	312 clientCountStr = clientCountFile.read(1)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	313 clientCount=string.atoi(clientCountStr)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	314 clientCount=clientCount+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	315 clientCountFile.close()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	316
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	317 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	318 clientCountFile.write('<count> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	319 clientCountFile.write(str(clientCount))
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	320 clientCountFile.write('</count> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	321
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	322
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	323
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	324
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	325 clientName = 'client_'+ str(clientCount)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	326
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	327 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/'+clientName+'.xml','w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	328 clientXml.seek(0,0)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	329
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	330 clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +'">\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	331 clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	332
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	333
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	334 clientXml.write(' <command interpreter="python">\n #client_1.py \n'+' $output \n ' +resUrl+'\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	335 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	336
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	337
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	338 j=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	339 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	340 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	341 clientXml.write(' '+self.formatString(param.getName())+'\n#if $source'+str(j)+'.source'+str(j)+'_source=="user" $source'+str(j)+'.user_param'+str(j)+' #else $source' + str(j) + '.cached_param' + str(j)+' #end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	342 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	343 clientXml.write('#if $cond_source.optional_param_source=="yes"')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	344
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	345 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	346 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	347 clientXml.write(' '+self.formatString(param.getName())+'\n#if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user" $cond_source.source'+str(j)+'.user_param'+str(j)+' #else $cond_source.source' + str(j) + '.cached_param' + str(j)+' #end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	348 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	349
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	350 clientXml.write('#else \n#end if\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	351 clientXml.write('</command>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	352
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	353 ##write inputs depending on required or not. if not required den dont display
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	354 ##if required- den check default value, and if options exist.Depending on that
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	355 ##decide the type of parameter and options
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	356 clientXml.write(' <inputs>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	357
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	358
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	359 j=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	360 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	361 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	362 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	363 if param.getOptionvalue().size()==0:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	364 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	365 if not param.getDefault1() == None:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	366 clientXml.write('value="'+param.getDefault1()+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	367 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	368 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	369 else:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	370 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	371 for option in param.getOptionvalue():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	372 clientXml.write(' <option value="'+self.formatString(option)+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	373 if option == param.getDefault1():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	374 clientXml.write('selected="true"')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	375 clientXml.write('>'+option+'</option>\n ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	376 clientXml.write(' </param> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	377 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	378 clientXml.write(' </when>\n')
d5cd409b8a18 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="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	380
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	381 clientXml.write(' <conditional name="cond_source">\n <param name="optional_param_source" type="select" label="Display Additional Parameters"> \n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param> \n <when value="no"> \n </when>\n <when value="yes"> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	382
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	383 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	384 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	385 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	386 if param.getOptionvalue().size()==0:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	387 clientXml.write(' <param format="text" size = "150" name = "user_param'+str(j)+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	388 if not param.getDefault1() == None:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	389 clientXml.write('value="'+param.getDefault1()+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	390 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	391 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	392 else:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	393 clientXml.write(' <param name="user_param'+str(j)+'" type="select" label="Select'+param.getName()+'" help="see tip below">\n' )
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	394 for option in param.getOptionvalue():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	395 clientXml.write(' <option value="'+self.formatString(option)+'" ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	396 if option == param.getDefault1():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	397 clientXml.write('selected="true"')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	398 clientXml.write('>'+option+'</option>\n ')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	399 clientXml.write(' </param> \n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	400 j=j+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	401 clientXml.write(' </when>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	402 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	403
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	404 clientXml.write(' </when>\n </conditional>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	405
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	406 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	407
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	408 clientXml.write(' <help>\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	409 for param in params:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	410 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	411 clientXml.write('\n.. class:: infomark\n\nTIP: About '+ param.getName() +': type is ' + param.getType())
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	412
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	413 modelRef = sawPD.getCompleteModelReference(param)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	414 if not modelRef is None:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	415 paramClass = dataFactory.getOWLClass(IRI.create(modelRef));
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	416 annotationSet = paramClass.getAnnotations(ontology,propertyComment)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	417 for annotation in annotationSet:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	418 if isinstance(annotation.getValue(),OWLLiteral):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	419 val = annotation.getValue()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	420 if val.isOWLStringLiteral() and not val.isOWLTypedLiteral():
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	421 print 'val.getLiteral()=' + val.getLiteral()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	422 clientXml.write(', description from ontology is "' + val.getLiteral()+'"')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	423 break
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	424 clientXml.write('\n')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	425 clientXml.write(' </help>\n</tool>')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	426 editor = editToolConfig()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	427 editor.addTool(clientName)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	428
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	429 ##later add help feature
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	430
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	431 def wsdlClient(self):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	432 ##parse wadl
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	433 javahome = os.environ.get('JAVA_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	434 galaxyhome=os.environ.get('GALAXY_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	435 classpath= galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/bin'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	436 jarpath = galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/lib/'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	437 machine = platform.machine()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	438
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	439 if machine == 'x86_64' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	440 print 'a'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	441 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	442 elif machine == 'i686' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	443 print 'b'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	444 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	445 elif machine == 'sun4u' :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	446 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	447 else :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	448 print 'c'
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	449 System.exit("Could not identify machine, please specify path to libjvm.so")
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	450
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	451
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	452 pkg=JPackage('lsdis')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	453 wsdlUrl = self.url
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	454
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	455 webserviceId = self.methodName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	456 resUrl = self.resourceName
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	457
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	458 urls = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	459 methods = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	460 params = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	461 paramTypes = []
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	462
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	463 WSDLParserDriver =pkg.WSDLParserDriver
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	464 wPD=WSDLParserDriver()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	465 wPD.parse(wsdlUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	466 methods = wPD.getCompleteMethodList()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	467 urls = wPD.getUrl()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	468
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	469 f=open(self.Ofile,'w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	470 f.write(wsdlUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	471 f.write('\n'+ resUrl)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	472 f.write('\n'+webserviceId)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	473
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	474
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	475 i=0
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	476 for method in methods:
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	477 x = str(method.getName().getLocalPart())
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	478 if x == webserviceId :
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	479 wPD.getParameters(x)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	480 f.write('method matched')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	481 paramTypes = wPD.getParamTypeList()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	482 params = wPD.getParamList()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	483 break
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	484 i=i+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	485
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	486
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	487
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	488
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	489 ##generate client's xml
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	490 galaxyhome=os.environ.get('GALAXY_HOME')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	491
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	492 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	493 clientCountFile.readline()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	494 clientCountStr = clientCountFile.read(1)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	495 clientCount=string.atoi(clientCountStr)
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	496 clientCount=clientCount+1
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	497 clientCountFile.close()
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	498
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	499 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository ganjoo parents: diff changeset	500 clientCountFile.write('<count> \n')

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_conf import *

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13

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14 class ClientGenerator(object):

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15

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16 #instantiate a client for invocation of the selected method of a Web service in workflows

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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 ./workflowclients/

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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

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63 urls = []

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64 methods = []

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65 params = []

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66

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67 #invoke the WADL parser packaged with this tool.

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68 WADLParserDriver=pkg.WADLParserDriver

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69 wPD=WADLParserDriver()

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70 wPD.parse(urlToPass)

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71 urls = wPD.getUrl()

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72 methods = wPD.getCompleteMethodList()

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73

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

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

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76 f.write(wadlUrl)

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

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

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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('\n in methods')

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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('\n method matched')

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88 f.write('\n y is' + y + ', resUrl is '+resUrl)

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89 if y == resUrl :

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90 f.write('res matched')

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

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92 break

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93 i=i+1

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94

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95

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96

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

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98

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

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100 #read the count and increment it.

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

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102 clientCountFile.readline()

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103 clientCountStr = clientCountFile.read(1)

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104 clientCount=string.atoi(clientCountStr)

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105 clientCount=clientCount+1

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106 clientCountFile.close()

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107

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

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

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110 clientCountFile.write(str(clientCount))

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

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112

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

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114 clientName = 'client_'+ str(clientCount)

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115

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116 #create a new xml file under ./workflowclients/

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

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118 clientXml.seek(0,0)

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119

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120 #write the tool id, name and description

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

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

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123

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124 #the workflow tool/client for a REST Web service invokes ./workflowclients/client_1.py to invoke the Web service

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

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

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127

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128

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129 j=0

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130 for param in params:

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131 if param.isRequired():

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132 clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')

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133 j=j+1

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134

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135 clientXml.write(' #else:\n $output\n ' +resUrl+'\n')

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136 j=0

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137 for param in params:

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138 if param.isRequired():

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139 clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')

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140 j=j+1

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141

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142 for param in params:

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143 if not param.isRequired():

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144 clientXml.write(' '+self.formatString(param.getName())+'\n #if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user":\n $cond_source.source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $cond_source.source' + str(j) + '.cached_param' + str(j)+'\n #end if\n')

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145 j=j+1

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146

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147 clientXml.write(' #end if\n')

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

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149

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150 #start writing inputs

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

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152

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153 #create a param for each required parameter described in the WADL. Check if defaults are specified. Create param such that

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154 #it can either be given a value manually or the value can be taken from a previous step.

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155 j=0

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156 for param in params:

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157 if param.isRequired():

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158 pName = param.getName()

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159 for doc in param.getDocs():

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

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161 pName = doc.getInnerText()

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162

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163 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')

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

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

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

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

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

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169 else:

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

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171 for option in param.getOptions():

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

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

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

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

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

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

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178 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>')

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179 j=j+1

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180

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181 #create a conditional param for each optional parameter described in the WADL. Again the param can be given a value manually or the value can be taken from

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182 #a previous step.

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

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184

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185 for param in params:

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186 if not param.isRequired():

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187 pName = param.getName()

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188 for doc in param.getDocs():

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

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190 pName = doc.getInnerText()

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191

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192 clientXml.write('\n<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n</param>\n <when value="user">')

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

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

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

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

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

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198 else:

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

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200 for option in param.getOptions():

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

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

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

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

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

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

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207 clientXml.write('<when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>\n')

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208 j=j+1

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209

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210

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211

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

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213

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214 #write information about each parameter in the help section

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

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

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217

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218 for param in params:

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219 if param.isRequired():

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220 pName = param.getName()

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221 for doc in param.getDocs():

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

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223 pName = doc.getInnerText()

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

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225

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

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227

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

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229 editor = editToolConfig()

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230 editor.addTool(clientName)

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231

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232

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233 def sawadlClient(self):

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234 ##parse sawadl

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

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

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

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

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239 machine = platform.machine()

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240

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241 #if machine == 'x86_64' :

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242 # print 'a'

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

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244 #elif machine == 'i686' :

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245 # print 'b'

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

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247 #elif machine == 'sun4u' :

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

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249 #else :

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250 # print 'c'

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

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252

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253

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

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

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

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

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258

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

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260

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261 sawadlUrl = self.url

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262

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263 webserviceId = self.methodName

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264 resUrl = self.resourceName

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265

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266 urls = []

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267 methods = []

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268 params = []

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269 annotationSet = []

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270

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271 SAWADLParserDriver=pkg.SAWADLParserDriver

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272 sawPD=SAWADLParserDriver()

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273 sawPD.parse(sawadlUrl)

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274 urls = sawPD.getUrl()

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275 methods = sawPD.getCompleteMethodList()

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276

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277 IRI = pkgModel.IRI

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278 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary

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279 OWLManager = pkgApiBinding.OWLManager

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280 OWLLiteral = pkgModel.OWLLiteral

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281 owlOntManager = OWLManager.createOWLOntologyManager()

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

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283 dataFactory = owlOntManager.getOWLDataFactory()

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

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285

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

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287 f.write(sawadlUrl)

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

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

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290

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291

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292 i=0

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293 for method in methods:

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294 x = str(method.getName())

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

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296 if x == webserviceId :

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297 f.write('method matched')

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298 if y == resUrl :

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299 f.write('res matched')

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

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301 break

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302 i=i+1

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303

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

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304

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

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305

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

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306

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

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307 ##generate client's xml

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

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309

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

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311 clientCountFile.readline()

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312 clientCountStr = clientCountFile.read(1)

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313 clientCount=string.atoi(clientCountStr)

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314 clientCount=clientCount+1

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315 clientCountFile.close()

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316

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

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

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319 clientCountFile.write(str(clientCount))

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

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321

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322

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323

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324

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

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325 clientName = 'client_'+ str(clientCount)

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326

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

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

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328 clientXml.seek(0,0)

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329

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

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

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

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332

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

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333

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

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

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

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336

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

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diff changeset

337

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

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diff changeset

338 j=0

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339 for param in params:

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

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341 clientXml.write(' '+self.formatString(param.getName())+'\n#if $source'+str(j)+'.source'+str(j)+'_source=="user" $source'+str(j)+'.user_param'+str(j)+' #else $source' + str(j) + '.cached_param' + str(j)+' #end if\n')

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342 j=j+1

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diff changeset

343 clientXml.write('#if $cond_source.optional_param_source=="yes"')

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344

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

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345 for param in params:

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diff changeset

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

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347 clientXml.write(' '+self.formatString(param.getName())+'\n#if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user" $cond_source.source'+str(j)+'.user_param'+str(j)+' #else $cond_source.source' + str(j) + '.cached_param' + str(j)+' #end if\n')

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348 j=j+1

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349

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350 clientXml.write('#else \n#end if\n')

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

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352

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

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

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355 ##decide the type of parameter and options

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

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357

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

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358

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

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359 j=0

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360 for param in params:

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

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362 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')

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diff changeset

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

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

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

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

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

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

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368 j=j+1

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diff changeset

369 else:

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

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371 for option in param.getOptionvalue():

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

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373 if option == param.getDefault1():

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

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

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

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377 j=j+1

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

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379 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>')

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380

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

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

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382

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

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383 for param in params:

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parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

385 clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n')

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

391 j=j+1

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

ganjoo

parents:

diff changeset

392 else:

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

394 for option in param.getOptionvalue():

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

396 if option == param.getDefault1():

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

400 j=j+1

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

402 clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>')

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

ganjoo

parents:

diff changeset

403

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

405

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

407

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

409 for param in params:

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

412

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

ganjoo

parents:

diff changeset

413 modelRef = sawPD.getCompleteModelReference(param)

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

ganjoo

parents:

diff changeset

414 if not modelRef is None:

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

416 annotationSet = paramClass.getAnnotations(ontology,propertyComment)

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

ganjoo

parents:

diff changeset

417 for annotation in annotationSet:

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

419 val = annotation.getValue()

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

423 break

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

ganjoo

parents:

diff changeset

424 clientXml.write('\n')

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

426 editor = editToolConfig()

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

ganjoo

parents:

diff changeset

427 editor.addTool(clientName)

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

ganjoo

parents:

diff changeset

428

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

ganjoo

parents:

diff changeset

429 ##later add help feature

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

ganjoo

parents:

diff changeset

430

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

ganjoo

parents:

diff changeset

431 def wsdlClient(self):

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

ganjoo

parents:

diff changeset

432 ##parse wadl

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

437 machine = platform.machine()

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

ganjoo

parents:

diff changeset

438

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

ganjoo

parents:

diff changeset

439 if machine == 'x86_64' :

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

ganjoo

parents:

diff changeset

440 print 'a'

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

442 elif machine == 'i686' :

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

ganjoo

parents:

diff changeset

443 print 'b'

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

445 elif machine == 'sun4u' :

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

447 else :

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

ganjoo

parents:

diff changeset

448 print 'c'

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

450

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

ganjoo

parents:

diff changeset

451

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

ganjoo

parents:

diff changeset

452 pkg=JPackage('lsdis')

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

ganjoo

parents:

diff changeset

453 wsdlUrl = self.url

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

ganjoo

parents:

diff changeset

454

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

ganjoo

parents:

diff changeset

455 webserviceId = self.methodName

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

ganjoo

parents:

diff changeset

456 resUrl = self.resourceName

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

ganjoo

parents:

diff changeset

457

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

ganjoo

parents:

diff changeset

458 urls = []

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

ganjoo

parents:

diff changeset

459 methods = []

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

ganjoo

parents:

diff changeset

460 params = []

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

ganjoo

parents:

diff changeset

461 paramTypes = []

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

ganjoo

parents:

diff changeset

462

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

ganjoo

parents:

diff changeset

463 WSDLParserDriver =pkg.WSDLParserDriver

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

ganjoo

parents:

diff changeset

464 wPD=WSDLParserDriver()

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

ganjoo

parents:

diff changeset

465 wPD.parse(wsdlUrl)

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

ganjoo

parents:

diff changeset

466 methods = wPD.getCompleteMethodList()

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

ganjoo

parents:

diff changeset

467 urls = wPD.getUrl()

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

ganjoo

parents:

diff changeset

468

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

470 f.write(wsdlUrl)

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

473

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

ganjoo

parents:

diff changeset

474

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

ganjoo

parents:

diff changeset

475 i=0

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

ganjoo

parents:

diff changeset

476 for method in methods:

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

478 if x == webserviceId :

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

ganjoo

parents:

diff changeset

479 wPD.getParameters(x)

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

ganjoo

parents:

diff changeset

480 f.write('method matched')

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

ganjoo

parents:

diff changeset

481 paramTypes = wPD.getParamTypeList()

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

ganjoo

parents:

diff changeset

482 params = wPD.getParamList()

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

ganjoo

parents:

diff changeset

483 break

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

ganjoo

parents:

diff changeset

484 i=i+1

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

ganjoo

parents:

diff changeset

485

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

ganjoo

parents:

diff changeset

486

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

ganjoo

parents:

diff changeset

487

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

ganjoo

parents:

diff changeset

488

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

ganjoo

parents:

diff changeset

489 ##generate client's xml

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

491

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

493 clientCountFile.readline()

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

ganjoo

parents:

diff changeset

494 clientCountStr = clientCountFile.read(1)

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

ganjoo

parents:

diff changeset

495 clientCount=string.atoi(clientCountStr)

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

ganjoo

parents:

diff changeset

496 clientCount=clientCount+1

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

ganjoo

parents:

diff changeset

497 clientCountFile.close()

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

ganjoo

parents:

diff changeset

498

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

501 clientCountFile.write(str(clientCount))

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

503

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

ganjoo

parents:

diff changeset

504

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

ganjoo

parents:

diff changeset

505

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

ganjoo

parents:

diff changeset

506

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

ganjoo

parents:

diff changeset

507 clientName = 'client_'+ str(clientCount)

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

ganjoo

parents:

diff changeset

508

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

510 clientXml.seek(0,0)

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

ganjoo

parents:

diff changeset

511

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

514

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

ganjoo

parents:

diff changeset

515

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

518

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

ganjoo

parents:

diff changeset

519 j=0

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

ganjoo

parents:

diff changeset

520 for param in params:

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

523 j=j+1

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

525

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

ganjoo

parents:

diff changeset

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

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

ganjoo

parents:

diff changeset

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

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

ganjoo

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diff changeset

528 ##decide the type of parameter and options

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

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

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

ganjoo

parents:

diff changeset

530

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

ganjoo

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diff changeset

531 j=0

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

ganjoo

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diff changeset

532 for param in params:

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

ganjoo

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diff changeset

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

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

ganjoo

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diff changeset

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

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

ganjoo

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diff changeset

535 j=j+1

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

ganjoo

parents:

diff changeset

536

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

ganjoo

parents:

diff changeset

537

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

ganjoo

parents:

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538

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

ganjoo

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diff changeset

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

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

ganjoo

parents:

diff changeset

540

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

ganjoo

parents:

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

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

ganjoo

parents:

diff changeset

542

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

ganjoo

parents:

diff changeset

543 j=0

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

ganjoo

parents:

diff changeset

544 for param in params:

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

ganjoo

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diff changeset

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

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

ganjoo

parents:

diff changeset

546

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

ganjoo

parents:

diff changeset

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

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

ganjoo

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548 editor = editToolConfig()

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

ganjoo

parents:

diff changeset

549 editor.addTool(clientName)

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

ganjoo

parents:

diff changeset

550

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

ganjoo

parents:

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551 ##later add help feature

Mercurial > repos > ganjoo > webservice_toolsuite

annotate WebServiceToolWorkflow/generateClient.py @ 0:d5cd409b8a18 default tip