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Merged
adrianq merged 7 commits into from
Sep 2, 2018
Merged

Load json models #71

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411feac
import json models
Aug 26, 2018
f83fef6
import models in json format
Aug 26, 2018
b561ad0
Merge branch 'development' into load_json_model
Aug 26, 2018
3344d3c
docker failing because of branch version
Aug 26, 2018
bfd98b4
remove variable
Aug 29, 2018
220249e
merge with development
Aug 29, 2018
6b3265b
remove print()
Sep 2, 2018
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57 changes: 39 additions & 18 deletions netpyne_ui/netpyne_geppetto.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,24 +109,45 @@ def importModel(self, modelParameters):
self.compileModMechFiles(modelParameters['compileMod'], modelParameters['modFolder'])

import netpyne_geppetto
# NetParams
netParamsPath = str(modelParameters["netParamsPath"])
sys.path.append(netParamsPath)
os.chdir(netParamsPath)
# Import Module
netParamsModuleName = importlib.import_module(str(modelParameters["netParamsModuleName"]))
# Import Model attributes
netpyne_geppetto.netParams = getattr(netParamsModuleName, str(modelParameters["netParamsVariable"]))

# SimConfig
simConfigPath = str(modelParameters["simConfigPath"])
sys.path.append(simConfigPath)
os.chdir(simConfigPath)
# Import Module
simConfigModuleName = importlib.import_module(str(modelParameters["simConfigModuleName"]))
# Import Model attributes
netpyne_geppetto.simConfig = getattr(simConfigModuleName, str(modelParameters["simConfigVariable"]))

if modelParameters['importFormat']=='py':
# NetParams
netParamsPath = str(modelParameters["netParamsPath"])
sys.path.append(netParamsPath)
os.chdir(netParamsPath)
# Import Module
netParamsModuleName = importlib.import_module(str(modelParameters["netParamsModuleName"]))
# Import Model attributes
netpyne_geppetto.netParams = getattr(netParamsModuleName, str(modelParameters["netParamsVariable"]))

for key, value in netpyne_geppetto.netParams.cellParams.iteritems():
if hasattr(value, 'todict'):
netpyne_geppetto.netParams.cellParams[key] = value.todict()

# SimConfig
simConfigPath = str(modelParameters["simConfigPath"])
sys.path.append(simConfigPath)
os.chdir(simConfigPath)
# Import Module
simConfigModuleName = importlib.import_module(str(modelParameters["simConfigModuleName"]))
# Import Model attributes
netpyne_geppetto.simConfig = getattr(simConfigModuleName, str(modelParameters["simConfigVariable"]))

elif modelParameters['importFormat']=='json':
with open(modelParameters['jsonModelFolder'], 'r') as file:
jsonData = json.load(file)

if 'net' in jsonData:
if 'params' in jsonData['net'] and 'simConfig' in jsonData:
netpyne_geppetto.netParams = specs.NetParams(jsonData['net']['params'])
netpyne_geppetto.simConfig = specs.SimConfig(jsonData['simConfig'])
netpyne_geppetto.netParams.cellParams = jsonData['net']['params']['cellParams']
else:
return self.getJSONError("Assertion error while importing the NetPyNE model", "The json file does not contain the following keys: [params, simConfig]")
else:
return self.getJSONError("Assertion error while importing the NetPyNE model", "The json file does not contain the following keys: [net]")
else:
return self.getJSONError("Assertion error while importing the NetPyNE model", "frontend sent a wrong option for 'importFormat'. allowed values are py and json")
return self.getJSONReply()
except:
return self.getJSONError("Error while importing the NetPyNE model",traceback.format_exc())
Expand Down Expand Up @@ -415,7 +436,7 @@ def deleteParam(self, paramToDel):

def validateFunction(self, functionString):
return utils.ValidateFunction(functionString, netParams.__dict__)

def generateScript(self, metadata):
def convert2bool(string):
return string.replace('true', 'True').replace('false', 'False')
Expand Down
2 changes: 1 addition & 1 deletion utilities/install.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def main(argv):
clone('https://github.com/openworm/pygeppetto.git','pygeppetto','v0.4.1-M1')
subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')

clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','0.7.9')
clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','v0.7.9')
subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')

clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','v0.4.1-M2','', True )
Expand Down