Merge pull request #126 from MetaCell/feature/125

Feature/125 update jupyter geppetto

Author: filippomc

netpyne_ui/netpyne_geppetto.py

@@ -98,7 +98,7 @@ def simulateNetPyNEModelInGeppetto(self, args):
                     logging.debug('Running single thread simulation')
                     netpyne_model = self.simulateNetPyNEModel()
 
-                return json.loads(GeppettoModelSerializer().serialize(self.geppetto_model))
+                return json.loads(GeppettoModelSerializer.serialize(self.geppetto_model))
         except:
             return utils.getJSONError("Error while simulating the NetPyNE model", sys.exc_info())
 

netpyne_ui/netpyne_model_interpreter.py

@@ -18,6 +18,7 @@ def getGeppettoModel(self, netpyne_model):
 
         # We create a GeppettoModel instance and we set a name a assign a lib
         geppetto_model = self.factory.createGeppettoModel('NetPyNEModel')
+        self.factory.geppetto_common_library = geppetto_model.libraries[0]
         netpyne_geppetto_library = pygeppetto.GeppettoLibrary(
             name='netpynelib')
         geppetto_model.libraries.append(netpyne_geppetto_library)
@@ -44,6 +45,7 @@ def extractPopulations(self, netpyne_model, netpyne_geppetto_library, geppetto_m
                     composite_id = cell['tags']['pop'] + "_cell"
 
                 cellType = pygeppetto.CompositeType(id=str(composite_id), name=str(composite_id), abstract= False)
+
                 visualType = pygeppetto.CompositeVisualType(id='cellMorphology', name='cellMorphology')
                 cellType.visualType = visualType
                 defaultValue = ArrayValue(elements=[])

run.py

@@ -0,0 +1,21 @@
+'''
+Run this to debug
+'''
+import sys
+import os
+from notebook.notebookapp import main, NotebookApp
+import netpyne_ui
+from jupyter_geppetto import settings
+
+settings.debug = True
+
+if __name__ == '__main__':
+    sys.argv.append('--NotebookApp.default_url=/geppetto')
+    sys.argv.append("--NotebookApp.token=''")
+    sys.argv.append('--library=netpyne_ui')
+
+    app = NotebookApp.instance()
+    app.initialize(sys.argv)
+    app.file_to_run = ''
+    sys.exit(app.start())
+

setup.py

@@ -37,7 +37,7 @@
         'Programming Language :: Python :: 3.7'
     ],
     install_requires=[
-        'jupyter_geppetto==0.4.2',
+        'jupyter-geppetto>=1.0.0',
         'netpyne==0.9.1.1'
     ],
 )

utilities/GeppettoConfiguration.json …lities/GeppettoConfiguration.copyme.jsonutilities/GeppettoConfiguration.json renamed to utilities/GeppettoConfiguration.copyme.json utilities/GeppettoConfiguration.json renamed to utilities/GeppettoConfiguration.copyme.json

@@ -1,6 +1,6 @@
 {
     "_README" : "http://docs.geppetto.org/en/latest/build.html",
-    "contextPath": "org.geppetto.frontend/",
+    "contextPath": "org.geppetto.frontend",
     "useSsl": false,
     "embedded": false,
     "embedderURL": ["/"],

utilities/install.py

@@ -27,7 +27,8 @@ def checkout(folder, default_branch, cwdp):
     newPath = currentPath+"/"+cwdp+folder
     print(newPath)
     os.chdir(newPath)
-    python_git=subprocess.Popen("git branch -a",shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+    python_git = subprocess.Popen("git branch -a && git tag", shell=True, stdout=subprocess.PIPE,
+                                  stderr=subprocess.PIPE)
     outstd,errstd=python_git.communicate()
     if branch and branch in str(outstd) and branch != 'development': # don't ckeckout development for netpyne
         subprocess.call(['git', 'checkout', branch], cwd='./')
@@ -45,25 +46,29 @@ def main(argv):
     main(sys.argv[1:])
 
 os.chdir(os.getcwd()+"/../")
-# Cloning Repos
-clone('https://github.com/openworm/pygeppetto.git','pygeppetto','development')
-subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')
+
 
 clone('https://github.com/Neurosim-lab/netpyne.git','netpyne','ui')
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./netpyne/')
 
-clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development')
-with open('npm_frontend_jupyter_log', 'a') as stdout:
-    subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout)
-subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js')
+
 
 # We can't clone org.geppetto.frontend as a regular submodule because Travis doesn't have .gitmodules in the zip
 # subprocess.call(['git', 'submodule', 'update', '--init'], cwd='./')
 clone('https://github.com/openworm/org.geppetto.frontend.git','geppetto','development','netpyne_ui/', False, 'geppetto')
 clone('https://github.com/MetaCell/geppetto-netpyne.git','geppetto-netpyne','development','netpyne_ui/geppetto/src/main/webapp/extensions/')
 
+branch = None
+# Cloning Repos
+clone('https://github.com/openworm/pygeppetto.git','pygeppetto','development')
+subprocess.call(['pip', 'install', '-e', '.'], cwd='./pygeppetto/')
+clone('https://github.com/openworm/org.geppetto.frontend.jupyter.git','org.geppetto.frontend.jupyter','development')
+with open('npm_frontend_jupyter_log', 'a') as stdout:
+    subprocess.call(['npm', 'install'], cwd='./org.geppetto.frontend.jupyter/js', stdout=stdout)
+subprocess.call(['npm', 'run', 'build-dev'], cwd='./org.geppetto.frontend.jupyter/js')
+
 print("Enabling Geppetto NetPyNE Extension ...")
-geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.json')
+geppetto_configuration = os.path.join(os.path.dirname(__file__), './utilities/GeppettoConfiguration.copyme.json')
 copyfile(geppetto_configuration, './netpyne_ui/geppetto/src/main/webapp/GeppettoConfiguration.json')
 
 # Installing and building
@@ -75,10 +80,10 @@ def main(argv):
 print("Installing jupyter_geppetto python package ...")
 subprocess.call(['pip', 'install', '-e', '.'], cwd='./org.geppetto.frontend.jupyter')
 print("Installing jupyter_geppetto Jupyter Extension ...")
-subprocess.call(['jupyter', 'nbextension', 'install', '--py', '--symlink', '--user', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
-subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--user', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
-subprocess.call(['jupyter', 'nbextension', 'enable', '--py', 'widgetsnbextension'], cwd='./org.geppetto.frontend.jupyter')
-subprocess.call(['jupyter', 'serverextension', 'enable', '--py', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'nbextension', 'install', '--py', '--symlink', '--sys-prefix', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'nbextension', 'enable', '--py', '--sys-prefix', 'widgetsnbextension'], cwd='./org.geppetto.frontend.jupyter')
+subprocess.call(['jupyter', 'serverextension', 'enable', '--sys-prefix', '--py', 'jupyter_geppetto'], cwd='./org.geppetto.frontend.jupyter')
 
 print("Installing NetPyNE UI python package ...")
 subprocess.call(['pip', 'install', '-e', '.'], cwd='.')