diff WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.py~ @ 0:049760c677de default tip

Galaxy WSExtensions added successfully

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.py~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,160 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+import warnings
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+
+    import sys
+    import os
+    import time
+    galaxyhome=os.environ.get('GALAXY_HOME')
+    sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')    
+    from creatorEngineComplex import *
+    from wsdl2path import *
+    from paramConverter import *
+    from ZSI.writer import SoapWriter
+    from collections import deque
+
+__author__="Shefali Shastri"
+
+def main():
+    """
+
+    This script takes the values of the input parameters of the
+    web service from the user and invokes the web service.
+    The URL to the WSDL is the command line argument
+
+    """
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+
+        #galaxyhome=os.environ.get('GALAXY_HOME')
+        #sys.path.append(galaxyhome+'/tools/SOAPclient/clients/clientGenerator/')
+        os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        webservice = str(sys.argv[5])
+        #print 'WS ', webservice
+        operation = str(sys.argv[6])
+        #print 'OP ',operation
+        resultfile=open(sys.argv[1],'w')
+        length=len(sys.argv)
+        inputdict={}
+        i=7
+        test=ClientCreator()
+        while(i>=7 and i<(length-1)):
+            key=sys.argv[i]
+            print 'key is : ',key
+            #if(sys.argv[i+1]=='ZSI.TC.String'):
+            val=sys.argv[i+1]
+            while(val.find('__at__')>-1):
+                vlist = val.split('__at__')
+                val = '@'.join(vlist)
+            while(val.find('__sq__')>-1):
+                vlist = val.split('__sq__')
+                val = ''.join(vlist)
+            while(val.find('__gt__')>-1):
+                vlist = val.split('__gt__')
+                val = '>'.join(vlist)
+            while(val.find('***')>-1):
+                vlist = val.split('***')
+                val = '\n'.join(vlist)
+            while(val.find('**')>-1):
+                vlist = val.split('**')
+                val = ' '.join(vlist)
+            while(val.find('__ob__')>-1):
+                vlist = val.split('__ob__')
+                val = '['.join(vlist)
+            while(val.find('__cb__')>-1):
+                vlist = val.split('__cb__')
+                val = ']'.join(vlist)
+            
+            print 'value is : ',val
+            
+                #if(val.find('__sq__')>-1):
+                 #   j=i+4
+                  #  val=val.lstrip('__sq__')
+                   # while(str(sys.argv[j]).find('__sq__')==-1):
+                    #    val=val+' '+sys.argv[j]
+                     #   j=j+1
+                    #val=val+' '+(str(sys.argv[j]).rstrip('__sq__'))
+                    #i=j-3
+
+            #elif((sys.argv[i+1]=='ZSI.TC.Integer')or (sys.argv[i+1]=='ZSI.TCnumbers.Iint')):
+             #   val=int(sys.argv[i+1])
+            #elif(sys.argv[i+1]=='ZSI.TC.Decimal'):
+             #   val=float(sys.argv[i+1])
+            #elif(sys.argv[i+2]=='Yes'):
+             #   valFile=open(sys.argv[i+3],'r')
+              #  val=valFile.read()
+            #else:
+             #   val=sys.argv[i+1]
+            if val == 'fileInput':
+                f = open(sys.argv[i+2])
+                #line = f.readline()
+                val = ''
+                #for j in line:
+                 #   val = val+j
+                #linestripped = line.strip('\n')
+                for line in f:
+                    #line = f.readline().strip('\n')
+                    #line = line.strip(' ')
+                    
+                    val = val+line
+                val = val.strip("\n")
+                print val
+                i = i+1
+                
+            if(val != "0"): 
+                inputdict[key] = val
+            #resultfile.write('value is :'+ val+'\n')
+            
+            i=i+2
+        print inputdict
+        if len(inputdict) == 0:
+            print 'empty inputs'
+            inputdic = {}
+        else:
+            inputdic = flat2nestedDict(inputdict)    
+        print 'the inputs are',inputdic
+        result = None
+        try:
+            result = test.invokeOp(operation,webservice,inputdic)
+        except:
+            pass
+        print 'The result before is ',result
+        #print ps
+        while result == None:
+            time.sleep(2)
+            print 'in loop'
+            result = test.invokeOp(operation,webservice,inputdic)
+        
+        print 'The result after is',result
+
+        # Writing the output to he o/p file when the result is parsed
+        for r in result:
+            if type(result[r])==list:
+                    for i in result[r]:
+                            resultfile.write(str(i)+'\n')
+                            print str(i)
+            else:
+                    resultfile.write(str(result[r])+'\n')
+
+        #Writes the result without parsinf in the XML format it gets.
+        #sw = SoapWriter(header=False, envelope=False);
+        #res = test.opname2outputClassOb(operation,webservice)
+        #res_tc = getattr(res,'typecode')
+        #ofwhat = res_tc.ofwhat;
+        #for tc in ofwhat :
+        #    sw.serialize(getattr(result, tc.aname), tc);
+        #    doc = sw.dom.getDocument();
+        #    fp = open(sys.argv[1], 'w');
+        #    try :
+        #        doc.writexml(fp, '\t', '', '\n');
+        #    finally :
+        #        fp.close();
+    
+
+
+
+if __name__ == "__main__":
+    main();
+