diff WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/clientGenerator/paramConverter.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/clientGenerator/paramConverter.py	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,198 @@
+'''
+@author  Rui Wnag, Chaitanya Guttula
+@see     LICENSE (MIT style license file).
+'''
+
+'''
+converter galaxy parameter <-----> user input dictionary for web service
+'|' is the seperator, if the real name contains it, it will cause wrong result in this converter
+'''
+from types import *
+#from galaxy.tools.parameters.basic import *
+
+__author__="Rui Wang"
+
+def nested2flatDict(nestedDic):
+    '''
+    nestedDic is dictionary e.g.{a:{a1:None, a2:None}, b:None, c:[{c1:None, c2:None},{c1:None, c2:None}]}, 
+    converter it into flatDict e.g.
+    {a|a1:TextToolParameter(), a|a2:TextToolParameter(), b:TextToolParameter(), 
+    c|1|c1:TextToolParameter(),c|1|c2:TextToolParameter(), c|2|c1:TextToolParameter(),c|2|c2:TextToolParameter()}
+    seperator is |, not /
+    '''
+    if nestedDic is None or len(nestedDic) == 0:
+        return {};
+    flatDic={}
+    
+    for key, value in nestedDic.iteritems():
+        if type(value) is DictType:
+            dicRecur(key, value, flatDic);
+        elif type(value) is ListType:
+            listRecur(key, value, flatDic);
+        elif value is None:
+            flatDic[key]=None#TextToolParameter(None, XML( '<param name="' + str(key) + '" type="text" size="10" value="default" />' ) )
+        else:
+            flatDic[key]=str(value)
+    return flatDic
+
+def dicRecur(prefix, dic, flatDic):
+    '''
+    '''
+    if dic is None or len(dic) == 0:
+        raise ValueError, 'dic is empty'
+    i=0;
+    for key, value in dic.items():
+        if type(value) is DictType:
+            #print key
+            dicRecur(prefix+"|"+key, value, flatDic);
+        elif type(value) is ListType:
+            listRecur(prefix+"|"+key, value, flatDic);
+        elif value is None:
+            #print 'key',key
+            #if (key.find('$')>-1):
+            #    vlist = key.split('$')
+            #    key = ''.join(vlist)
+            
+                #print 'key',key
+           #     flatDic[prefix+"|_"+str(i)+"|"+key]=None
+            #    i=i+1
+            #else:
+            flatDic[prefix+"|"+key]=None#TextToolParameter(None, XML( '<param name="' + str(prefix) + '|' + str(key) + '" type="text" size="10" value="default" />' ) )
+        else:
+            #print prefix
+            #if (key.find('$')>-1):
+            #    vlist = key.split('$')
+            #    key = ''.join(vlist)
+            
+            #    print 'key',key
+            #    flatDic[prefix+"|_"+str(i)+"|"+key]=None
+            #    i=i+1
+            #else:
+                flatDic[prefix+"|"+key]=str(value)
+            
+def listRecur(prefix, list, flatDic):
+    ''''''
+    
+    #You are expecting this list to contain a complexType.
+    #When it doesn't you raise a ValueError.
+    #If the list contains a simpletype then we add |$|
+    # when flatenning.
+    if list is None or len(list)==0:
+        flatDic[prefix+'|$|'] = [];
+        return [];
+    i=0
+    for value in list:
+        if type(value) is DictType:
+            #print prefix
+            dicRecur(prefix+"|"+str(i), value, flatDic);
+        #else:#if type(value) is ListType:
+         #   if prefix+'|0|' not in flatDic:
+        #        flatDic[prefix+'|0|'] = []
+        #    flatDic[prefix+'|0|'].append(value)
+        #    return ;
+            i += 1;
+
+def flat2nestedDict(flatDic):
+    '''the flatDic has value in it
+    converter it to nested dictionary'''
+    if flatDic is None or flatDic=={}: 
+        raise ValueError, 'flatDic is empty'
+    nestedDic = {};
+    for key, value in flatDic.iteritems() :
+        key_arr = key.split('|');
+        print key_arr
+        last_idx = len(key_arr) - 1;
+        sub_dic = nestedDic;
+        if last_idx != 0 :
+            i = 0;
+            # Iterates over the split values of a single key
+            while i < last_idx :
+                
+                try :
+                    key_int = int(key_arr[i]); # checking if the split value of key is number (true only if it )
+                    if key_int >= len(sub_dic) :
+                        for j in range(key_int - len(sub_dic) + 1) :
+                            sub_dic.append({});
+                    sub_dic = sub_dic[key_int];
+                 
+                except ValueError :
+ 
+                    #If the split value is not present in thhe subdic
+                    if key_arr[i] == '$':
+                      print '$ is there'#,nestedDic  
+                    else:
+                      if key_arr[i] not in sub_dic :
+                        try :
+                            key_int = int(key_arr[i + 1]); # Ckecking of the next split value in key is number
+                            
+                            # Executed if the key is or array type key
+                            sub_list = [];
+                            sub_dic[key_arr[i]] = sub_list;                            
+                            for j in range(key_int + 1) :
+                                sub_list.append({});
+                            sub_dic = sub_list[key_int];
+                            i += 1;
+                            
+                        except ValueError : # 2 consicutive split values in key are not numerical value (i.e not array)
+                            if key_arr[last_idx-1] == '$' :
+                                if i == last_idx-2 :
+                                    print 'Found the value',key_arr[i]
+                                else:
+                                    temp = {};
+                                    sub_dic[key_arr[i]] = temp;
+                                    sub_dic = temp;
+                                    
+                            else:   
+                                temp = {};
+                                sub_dic[key_arr[i]] = temp;
+                                sub_dic = temp;
+                                    
+                    # If the split value is present in the subdir then create a new subdic with
+                      else :  
+                        sub_dic = nestedDic[key_arr[i]];
+                        
+                i += 1;
+        if value == '' :
+            value = None;
+        if key_arr[last_idx-1] == '$':
+            templist=[];
+            if value != []: 
+                if value.find(',')>-1:
+                    vlist = value.split(',')
+                    for l in vlist:
+                        templist.append(l);
+                else:
+                    templist.append(value);
+            sub_dic[key_arr[last_idx-2]] = templist;
+        else:
+            sub_dic[key_arr[last_idx]] = value;
+            
+        # If the leaf node is basic array type
+        #if key_arr[last_idx] == '':
+        #    sub_dic[key_arr[last_idx-2]].append(value);
+        #else:
+        #    sub_dic[key_arr[last_idx]] = value;            
+        
+    return nestedDic
+            
+#testing this module only, before run below test, please comment line 6,30,33,50,53, and uncomment line 29,32,49,52, since they will use other modules of galaxy
+if __name__=="__main__":
+
+#    nestedDic={'_params':{ '_program' : 'blastp', '_database' :'swissprot', '_email' :'[e-mail]', '_async': 1}, '_content':[{'_type':'sequence', '_content':'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'},{'_type':'ss', '_content':'bbbbbbbbbbbbbbbb'}]}
+    nestedDic={'_params':{ '_program' : 'blastp', '_database' :{'_string':[]}, '_email' :'[e-mail]', '_async': '', '_test':[{'_name':'chaithu'},{'_name':'srinivas'}]}, '_content':[{'_type':'sequence', '_content':'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'},{'_type':'ss', '_content':'bbbbbbbbbbbbbbbb'}]}
+    #flatdic = nested2flatDict(nestedDic)
+    #print flatdic
+    flatDic={'_parameters|_program': 'blastp', '_parameters|_stype': 'protein', '_parameters|_sequence': 'MKLSKRYRFWQKVIKALGVLALIATLVLVVYLYKLGILNDSNELKDLVHKYEFWGPMIFIVAQIVQIVFPVIPGGVTTVAGFLIFGPTLGFIYNYIGIIIGSVILFWLVKFYGRKFVLLF', '_email': '[e-mail]', '_parameters|_database|_string|$|': 'uniprotkb,swissprot'}
+#{'_params|_email': '[e-mail]', '_params|_database': 'swissprot', '_params|_async': '1', '_content|0|_type': 'sequence', '_content|1|_type': 'ss','_params|_program|0|': 'hrllo', '_content|1|_content':'bbbbbbbbbbbbbbbb', '_content|0|_content': 'aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa'}
+    print flat2nestedDict(flatDic)
+            
+            
+            
+            
+            
+            
+            
+            
+            
+            
+