merged latest development

Author: enicolasgomez

netpyne_ui/experiments.py

@@ -154,7 +154,7 @@ def get_model_specification(name: str, trial: str) -> dict:
     """
     path = get_trial_output_path(name, trial, fallback=True)
     if path is None or not os.path.exists(path):
-        raise ExperimentsError(f"Trial file {path} not found")
+        raise ExperimentsError(f"Condition file {path} not found")
 
     with open(path, "r") as f:
         trial_output = json.load(f)
@@ -273,7 +273,7 @@ def onerror(func, path, exc_info):
 
 
 def _create_base_model_trial() -> model.Trial:
-    return model.Trial(name="Trial 1", id=BASE_TRIAL_ID)
+    return model.Trial(name="Condition 1", id=BASE_TRIAL_ID)
 
 
 def _create_trials(experiment: model.Experiment) -> List[model.Trial]:
@@ -315,7 +315,7 @@ def _create_trials(experiment: model.Experiment) -> List[model.Trial]:
 
         filename = combinations["filenames"][combIdx][1:]
         indices = combinations["indices"][combIdx]
-        name = f"Trial {combIdx + 1}"
+        name = f"Condition {combIdx + 1}"
 
         trials.append(
             model.Trial(name=name, params=params, indices=indices, id=filename)

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
@@ -138,7 +139,7 @@ def viewExperimentResult(self, payload: dict):
 
         file = experiments.get_trial_output_path(name, trial)
         if file is None or not os.path.exists(file):
-            return utils.getJSONError(f"Couldn't find output file of trial. Please take a look at the simulation log.", "")
+            return utils.getJSONError(f"Couldn't find output file of condition. Please take a look at the simulation log.", "")
 
         if self.doIhaveInstOrSimData()['haveInstance']:
             sim.clearAll()
@@ -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)

package.json

@@ -20,6 +20,7 @@ ipython-genutils==0.2.0
 ipywidgets==7.5.1
 jedi==0.17.0
 Jinja2==2.11.2
+jsonpickle==2.1.0
 jsonschema==3.2.0
 jupyter==1.0.0
 jupyter-client==6.1.3

requirements.txt

@@ -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()