Merged hrani changes and mine from new bindings. (#412)

removed 'basestring'

Co-authored-by: Dilawar Singh <dilawars@ncbs.res.in>

Author: dilawar

python/moose/genesis/writeKkit.py

@@ -10,6 +10,7 @@
 __email__            = "hrani@ncbs.res.in"
 __status__           = "Development"
 __updated__          = "Jan 08 2020"
+
 #Jan 8: added a line to add compartment info
 #       permeability from moose is in uM which to be converted to mM for genesis
 #2020
@@ -253,7 +254,7 @@ def writeConcChan(modelpath,f,sceneitems):
             if len(moose.element(cChan).neighbors['setNumChan']) == 1:
                 chanParent = moose.element(moose.element(cChan).neighbors['setNumChan'][0])
 
-            if not (isinstance(chanParent,moose.PoolBase)):
+            if not chanParent.isA['PoolBase']:
                 print(" raise exception Channel doesn't have pool as parent %s",moose.element(cChan).path)
                 return False,"raise exception Channel doesn't have pool as parent"
             else:
@@ -307,7 +308,7 @@ def writeEnz( modelpath,f,sceneitems):
             if len(moose.element(enz).neighbors['enzDest']) == 1:
                 enzParent = moose.element(moose.element(enz).neighbors['enzDest'][0])
 
-            if not (isinstance(enzParent,moose.PoolBase)):
+            if not enzParent.isA['PoolBase']:
                 print(" raise exception enz doesn't have pool as parent %s",moose.element(enz).path)
                 return False
             else:
@@ -431,29 +432,28 @@ def writeReac(modelpath,f,sceneitems):
     return reacList,error
 
 def trimPath(mobj):
-    original = mobj
     mobj = moose.element(mobj)
-    found = False
-    while not isinstance(mobj,moose.ChemCompt) and mobj.path != "/":
+    original = mobj
+    while not mobj.isA['ChemCompt'] and mobj.path != "/":
         mobj = moose.element(mobj.parent)
-        found = True
+
     if mobj.path == "/":
-        print(original, " object doesn't have compartment as a parent ")
+        print("%s object doesn't have a parent compartment as a parent." % original)
         return
-    #other than the kinetics compartment, all the othername are converted to group in Genesis which are place under /kinetics
+
+    # other than the kinetics compartment, all the othername are converted to group in Genesis which are place under /kinetics
     # Any moose object comes under /kinetics then one level down the path is taken.
     # e.g /group/poolObject or /Reac
-    if found:
-        if mobj.name != "kinetics":# and ( (mobj.className != "CubeMesh") and (mobj.className != "CylMesh") and (mobj.className != "EndoMesh") and (mobj.className != "NeuroMesh")):
-            splitpath = original.path[(original.path.find(mobj.name)):len(original.path)]
-        else:
-            pos = original.path.find(mobj.name)
-            slash = original.path.find('/',pos+1)
-            splitpath = original.path[slash+1:len(original.path)]
-        splitpath = re.sub(r"\[[0-9]+\]", "", splitpath)
-        s = splitpath.replace("_dash_",'-')
-        s = splitpath.replace("_space_","_")
-        return s
+    if mobj.name != "kinetics":# and ( (mobj.className != "CubeMesh") and (mobj.className != "CylMesh") and (mobj.className != "EndoMesh") and (mobj.className != "NeuroMesh")):
+        splitpath = original.path[(original.path.find(mobj.name)):len(original.path)]
+    else:
+        pos = original.path.find(mobj.name)
+        slash = original.path.find('/',pos+1)
+        splitpath = original.path[slash+1:len(original.path)]
+    splitpath = re.sub(r"\[[0-9]+\]", "", splitpath)
+    s = splitpath.replace("_dash_",'-')
+    s = splitpath.replace("_space_","_")
+    return s
 
 # def writeSumtotal( modelpath,f):
 #     funclist = moose.wildcardFind(modelpath+'/##[ISA=Function]')
@@ -585,22 +585,24 @@ def writePool(modelpath,f,volIndex,sceneitems):
 
     for p in moose.wildcardFind(modelpath+'/##[0][ISA=PoolBase]'):
         if findCompartment(p) == moose.element('/'):
-            error = error + " \n "+p.path+ " doesn't have compartment ignored to write to genesis"
+            error += "\n%s doesn't have compartment ignored to write to genesis" % p
         else:
             slave_enable = 0
-            if (p.className == "BufPool" or p.className == "ZombieBufPool"):
+            if p.isA["BufPool"] or p.isA["ZombieBufPool"]:
                 pool_children = p.children
                 if pool_children== 0:
                     slave_enable = 4
                 else:
                     for pchild in pool_children:
-                        if not(pchild.className == "ZombieFunction") and not(pchild.className == "Function"):
+                        if (not pchild.isA["ZombieFunction"]) and (not pchild.isA["Function"]):
                             slave_enable = 4
                         else:
                             slave_enable = 0
                             break
-            if (p.parent.className != "Enz" and p.parent.className !='ZombieEnz'):
-                #Assuming "p.parent.className !=Enzyme is cplx which is not written to genesis"
+
+            pp = moose.element(p.parent)
+            if (not pp.isA['Enz']) and (not pp.isA['ZombieEnz']):
+                # Assuming "p.parent.className !=Enzyme is cplx which is not written to genesis"
 
                 # x = sceneitems[p]['x']
                 # y = sceneitems[p]['y']