Merge branch 'development' of https://github.com/MetaCell/netpyne-ui into feature/389

Author: ddelpiano

netpyne_ui/netpyne_geppetto.py

@@ -14,6 +14,7 @@
 from shutil import copyfile
 from dacite import from_dict
 import base64
+import jsonpickle
 
 import neuron
 import numpy as np
@@ -184,7 +185,7 @@ def instantiateNetPyNEModelInGeppetto(self, args):
                     self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
 
                 return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model))
-        except Exception:
+        except Exception as e:
             message = "Error while instantiating the NetPyNE model"
             logging.exception(message)
             return utils.getJSONError(message, sys.exc_info())
@@ -266,6 +267,7 @@ def simulateNetPyNEModelInGeppetto(self, args):
         """
         allTrials = args.get('allTrials', True)
         use_prev_inst = args.get('usePrevInst', False)
+        sim_id = args.get('simId', 0)
 
         try:
             experiment = experiments.get_current()
@@ -289,17 +291,17 @@ def simulateNetPyNEModelInGeppetto(self, args):
                         return self.simulate_single_model(experiment, use_prev_inst)
                 except Exception:
                     experiment.state = model.ExperimentState.ERROR
-                    message = "Unknown error during simulation of Experiment"
+                    message = ("Unknown error during simulation of Experiment. SimulationId %i" % sim_id)
                     logging.exception(message)
-                    return utils.getJSONError("Unknown error during simulation of Experiment", sys.exc_info())
+                    return utils.getJSONError("Unknown error during simulation of Experiment", sys.exc_info(), { "sim_id": sim_id})
 
             else:
                 return self.simulate_single_model(use_prev_inst=use_prev_inst)
 
-        except Exception:
-            message = "Error while simulating the NetPyNE model"
+        except Exception as e :
+            message = ("Error while simulating the NetPyNE model: %s. SimulationId %f" % (e, sim_id))
             logging.exception(message)
-            return utils.getJSONError(message, sys.exc_info())
+            return utils.getJSONError(message, sys.exc_info(), { "sim_id": sim_id})
 
     def _prepare_simulation_files(self, experiment: model.Experiment = None, use_prev_inst: bool = False) -> str:
         """Prepares template files and netpyne model files for a single simulation """
@@ -647,6 +649,8 @@ def instantiateNetPyNEModel(self):
             saveData = sim.allSimData if hasattr(sim, 'allSimData') and 'spkt' in sim.allSimData.keys() and len(
                 sim.allSimData['spkt']) > 0 else False
 
+            #netcoded = jsonpickle.encode(self.netParams, unpicklable=False)
+            #simcoded = jsonpickle.encode(self.simConfig, unpicklable=False)
             sim.create(self.netParams, self.simConfig)
             sim.net.defineCellShapes()  # creates 3d pt for cells with stylized geometries
             sim.gatherData(gatherLFP=False)

tests/backend/netypne_model_importer_test.py

@@ -36,6 +36,7 @@ def setUpClass(cls):
             logging.error("Error loading mechanisms", exc_info=True)
 
     def test_dict_import_1(self):
+        assert 0
         print("------------------------------------")
         print("Dictionary transform importModel:")
         print("------------------------------------")
@@ -60,6 +61,40 @@ def test_dict_import_1(self):
         netpyne = NetPyNEGeppetto()
         netpyne.importModel(netpyne_info)
 
+    def test_netpyne_exported_model_1(self):
+      print("------------------------------------")
+      print("Netpyne exported model sim run")
+      print("------------------------------------")
+
+      params = {}
+
+      HERE = os.path.dirname(os.path.realpath(__file__))
+      ROOT = os.path.dirname(HERE)
+
+      params["areModFieldsRequired"] = False
+      params["compileMod"] = False
+      params["exploreOnlyDirs"] = False
+      params["explorerDialogOpen"] = False
+      params["explorerParameter"] = ""
+      params["freezeInstance"] = True
+      params["freezeSimulation"] = True
+      params["jsonModelFolder"] = ROOT + "/workspace/HHCellNetwork.txt_data.json"
+      params["jsonPath"] = ""
+      params["loadNet"] = True
+      params["loadNetParams"] = True
+      params["loadSimCfg"] = True
+      params["loadSimData"] = True
+      params["modFolder"] = ""
+      params["modPath"] = ""
+      params["tab"] = "simulate"
+
+      netpyne = NetPyNEGeppetto()
+
+      netpyne.loadModel(params)
+      netpyne.instantiateNetPyNEModel()
+
+      return False
+
 if __name__ == '__main__':
     try:
         unittest.main()