Polish import export

Author: rodriguez-facundo

netpyne_ui/api.py

@@ -116,19 +116,3 @@ def downloads(handler: IPythonHandler):
                     send_files(handler, tar_gz_file_path, tar_gz_file_name)
 
         handler.finish()
-
-    @get('/export')
-    def exportModel(self, args):
-        try:
-            with redirect_stdout(sys.__stdout__):
-                if not args['netCells']:
-                    sim.initialize(netParams = self.netParams, simConfig = self.simConfig)    
-                sim.cfg.filename = args['fileName']
-                include = [el for el in specs.SimConfig().saveDataInclude if el in args.keys() and args[el]]
-                if args['netCells']: include += ['netPops']
-                sim.cfg.saveJson = True
-                sim.saveData(include)
-                sim.cfg.saveJson = False
-            return utils.getJSONReply()
-        except:
-            return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info())

netpyne_ui/netpyne_geppetto.py

@@ -59,7 +59,7 @@ def instantiateNetPyNEModelInGeppetto(self, args):
                     netpyne_model = self.instantiateNetPyNEModel()
                     self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
 
-                return json.loads(GeppettoModelSerializer().serialize(self.geppetto_model))
+                return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model))
         except:
             return utils.getJSONError("Error while instantiating the NetPyNE model", sys.exc_info())
 
@@ -185,7 +185,7 @@ def remove(dictionary):
                         sim.loadSimData(args['jsonModelFolder'])
                     self.geppetto_model = self.model_interpreter.getGeppettoModel(sim)
 
-                    return json.loads(GeppettoModelSerializer().serialize(self.geppetto_model))
+                    return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model))
                 else:
                     return utils.getJSONReply()
         except:
@@ -263,6 +263,11 @@ def exportModel(self, args):
                 sim.cfg.saveJson = True
                 sim.saveData(include)
                 sim.cfg.saveJson = False
+
+                with open(f"{sim.cfg.filename}.json") as json_file:
+                    data = json.load(json_file)
+                    return data
+
             return utils.getJSONReply()
         except:
             return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info())
@@ -281,24 +286,31 @@ def importNeuroML(self, modelParams):
                 sim.initialize()
                 sim.importNeuroML2(modelParams['neuroMLFolder'], simConfig=specs.SimConfig(), simulate=False, analyze=False)
                 self.geppetto_model = self.model_interpreter.getGeppettoModel(sim)
-            return json.loads(GeppettoModelSerializer().serialize(self.geppetto_model))
+            return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model))
 
         except:
             return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info())
 
     def deleteModel(self, modelParams):
+        
         try:
             with redirect_stdout(sys.__stdout__):       
                 self.netParams = specs.NetParams()
                 self.simConfig = specs.SimConfig()
-                self.netParams.todict()
-                self.netParams.todict()
-                if self.doIhaveInstOrSimData()['haveInstance']: sim.clearAll()
+                sim.initialize(specs.NetParams(), specs.SimConfig())
                 self.geppetto_model = None
-            return utils.getJSONReply()
-
         except:
             return utils.getJSONError("Error while exporting the NetPyNE model", sys.exc_info())
+
+        try:
+            # This function fails is some keys don't exists
+            # sim.clearAll()
+            self.clearSim()
+            
+        except:
+            pass
+
+        return utils.getJSONReply()
 
     def instantiateNetPyNEModel(self):
         with redirect_stdout(sys.__stdout__):
@@ -542,7 +554,8 @@ def header(title, spacer='-'):
 
                 script.write(header('end script', spacer='='))
 
-            return utils.getJSONReply()
+            with open(fname) as f: 
+                return f.read()
 
         except:
             return utils.getJSONError("Error while importing the NetPyNE model", sys.exc_info())
@@ -649,6 +662,52 @@ def propagate_syn_mech_rename(self, new, old):
                                     self.netParams.stimTargetParams[label]['synMech'] = new
 
 
+    def clearSim(self):
+        # clean up
+        sim.pc.barrier()
+        sim.pc.gid_clear()                    # clear previous gid settings
+
+        # clean cells and simData in all nodes
+        sim.clearObj([cell.__dict__ if hasattr(cell, '__dict__') else cell for cell in sim.net.cells])
+        if 'stims' in list(sim.simData.keys()):
+            sim.clearObj([stim for stim in sim.simData['stims']])
+
+        for key in list(sim.simData.keys()): del sim.simData[key]
+
+        if hasattr(sim, 'net'):
+            for c in sim.net.cells: del c
+            for p in sim.net.pops: del p
+            if hasattr(sim.net, 'params'):
+                del sim.net.params
+
+
+        # clean cells and simData gathered in master node
+        if sim.rank == 0:
+            if hasattr(sim.net, 'allCells'):
+                sim.clearObj([cell.__dict__ if hasattr(cell, '__dict__') else cell for cell in sim.net.allCells])
+            if hasattr(sim, 'allSimData'):
+                if 'stims' in list(sim.allSimData.keys()):
+                    sim.clearObj([stim for stim in sim.allSimData['stims']])
+                for key in list(sim.allSimData.keys()): del sim.allSimData[key]
+                del sim.allSimData
+            
+            
+            import matplotlib
+            matplotlib.pyplot.clf()
+            matplotlib.pyplot.close('all')
+
+        if hasattr(sim, 'net'):
+            if hasattr(sim.net, 'allCells'):
+                for c in sim.net.allCells: del c
+                del sim.net.allCells
+            if hasattr(sim.net, 'allPops'):
+                for p in sim.net.allPops: del p
+
+            del sim.net
+
+        import gc; gc.collect()
+
+
 logging.info("Initialising NetPyNE UI")
 netpyne_geppetto = NetPyNEGeppetto()
 logging.info("NetPyNE UI initialised")