#277 refactor: moved generic mod file loading to utils_test.py

Author: filippomc

netpyne_ui/mod_utils.py

@@ -0,0 +1,42 @@
+import subprocess
+import os
+
+import neuron
+from neuron import h
+
+
+def is_loaded_mechanisms():
+    # copied from:
+    # https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/mechtype.html
+    mt = h.MechanismType(0)
+    mname = h.ref('')
+    mnames = list()
+    for i in range(mt.count()):
+        mt.select(i)
+        mt.selected(mname)
+        mnames.append(mname[0])
+
+    # note this check only works for the original hnn model
+    # need to generalize for any model
+
+    if 'hh2' not in mnames:
+        return False
+    else:
+        return True
+
+
+def compileModMechFiles(compileMod, modFolder):
+    # Create Symbolic link
+    if compileMod:
+        modPath = os.path.join(str(modFolder), "x86_64")
+
+        subprocess.call(["rm", "-r", modPath])
+
+        os.chdir(modFolder)
+        subprocess.call(["nrnivmodl"])
+        os.chdir('..')
+
+        try:
+            neuron.load_mechanisms(str(modFolder))
+        except:
+            raise

netpyne_ui/netpyne_geppetto.py

@@ -24,6 +24,7 @@
 from jupyter_geppetto import jupyter_geppetto, synchronization, utils
 from contextlib import redirect_stdout
 from netpyne_ui.constants import NETPYNE_WORKDIR_PATH, NUM_CONN_LIMIT
+from netpyne_ui.mod_utils import compileModMechFiles
 
 os.chdir(NETPYNE_WORKDIR_PATH)
 
@@ -114,20 +115,7 @@ def simulateNetPyNEModelInGeppetto(self, args):
         except:
             return utils.getJSONError("Error while simulating the NetPyNE model", sys.exc_info())
 
-    def compileModMechFiles(self, compileMod, modFolder):
-        # Create Symbolic link
-        if compileMod:
-            modPath = os.path.join(str(modFolder), "x86_64")
 
-            subprocess.call(["rm", "-r", modPath])
-
-            os.chdir(modFolder)
-            subprocess.call(["nrnivmodl"])
-            os.chdir('..')
-
-        # Load mechanism if mod path is passed
-        if modFolder:
-            neuron.load_mechanisms(str(modFolder))
 
     def loadModel(self, args):
         """ Imports a model stored as file in json format.
@@ -151,7 +139,7 @@ def remove(dictionary):
 
         try:
             owd = os.getcwd()
-            self.compileModMechFiles(args['compileMod'], args['modFolder'])
+            compileModMechFiles(args['compileMod'], args['modFolder'])
         except:
             return utils.getJSONError("Error while importing/compiling mods", sys.exc_info())
         finally:
@@ -222,7 +210,7 @@ def importModel(self, modelParameters):
             # Get Current dir
             owd = os.getcwd()
 
-            self.compileModMechFiles(modelParameters['compileMod'], modelParameters['modFolder'])
+            compileModMechFiles(modelParameters['compileMod'], modelParameters['modFolder'])
 
             with redirect_stdout(sys.__stdout__):
                 # NetParams
@@ -262,7 +250,7 @@ def importCellTemplate(self, modelParameters):
 
                 conds = {} if rule not in self.netParams.cellParams else self.netParams.cellParams[rule]['conds']
 
-                self.compileModMechFiles(modelParameters["compileMod"], modelParameters["modFolder"])
+                compileModMechFiles(modelParameters["compileMod"], modelParameters["modFolder"])
 
                 del modelParameters["modFolder"]
                 del modelParameters["compileMod"]