Merged conflicts

Author: vidhyalongani

Dockerfile

@@ -46,7 +46,7 @@ RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
 RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
 RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
 
-RUN python utilities/install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION} --netpyne $NETPYNE_VERSION --workspace WORKSPACE_VERSION --npm-skip
+RUN python utilities/install.py ${BUILD_ARGS} --geppetto ${GEPPETTO_VERSION} --workspace WORKSPACE_VERSION --npm-skip
 
 RUN jupyter labextension disable @jupyterlab/hub-extension
 

netpyne_ui/mod_utils.py

@@ -28,17 +28,22 @@ def is_loaded_mechanisms():
 
 def loadModMechFiles(compileMod, modFolder):
     # Create Symbolic link
-    if compileMod:
-        modPath = os.path.join(str(modFolder), "x86_64")
-
-        if os.path.exists(modPath):
-            shutil.rmtree(modPath)
 
-        os.chdir(modFolder)
-        subprocess.call(["nrnivmodl"])
-        os.chdir('..')
-
-    try:
-        neuron.load_mechanisms(str(modFolder))
-    except:
-        raise
+    if compileMod:
+        try:
+            owd = os.getcwd()
+            modPath = os.path.join(str(modFolder), "x86_64")
+
+            if os.path.exists(modPath):
+                shutil.rmtree(modPath)
+
+            os.chdir(modFolder)
+            subprocess.call(["nrnivmodl"])
+            os.chdir('..')
+
+            try:
+                neuron.load_mechanisms(str(modFolder))
+            except:
+                raise
+        finally:
+            os.chdir(owd)

netpyne_ui/netpyne_geppetto.py

@@ -13,6 +13,7 @@
 import json
 import logging
 import os
+from pathlib import Path
 import pprint
 import re
 import sys
@@ -511,7 +512,32 @@ def _create3D_shapes(self, json_path: str):
                 # Load again because gatherData removed simData
                 sim.loadSimData(json_path)
 
+    def loadFromIndexFile(self, json_path: str):
+        cfg, netParams = sim.loadModel(json_path, loadMechs=True, ignoreMechAlreadyExistsError=True)
+        self.simConfig = cfg
+        self.netParams = netParams
 
+        if isinstance(self.netParams, dict):
+          self.netParams = specs.NetParams(self.netParams)
+
+        if isinstance(self.simConfig, dict):
+          self.simConfig = specs.SimConfig(self.simConfig)
+
+        for key, value in self.netParams.cellParams.items():
+            if hasattr(value, 'todict'):
+                self.netParams.cellParams[key] = value.todict()
+
+        # TODO: when should sim.initialize be called?
+        #   Only on import or better before every simulation or network instantiation?
+        sim.initialize()
+
+    def saveToIndexFile(self, srcPath, dstPath, exportNetParamsAsPython, exportSimConfigAsPython):
+        sim.saveModel(netParams=self.netParams,
+                      simConfig=self.simConfig,
+                      srcPath=srcPath,
+                      dstPath=dstPath,
+                      exportNetParamsAsPython=exportNetParamsAsPython,
+                      exportSimConfigAsPython=exportSimConfigAsPython)
 
     def importModel(self, modelParameters):
         """ Imports a model stored in form of Python files.
@@ -575,7 +601,7 @@ def importModel(self, modelParameters):
 
     def importNeuroML(self, modelParameters):
         from netpyne_ui.helpers import neuroml
-       
+
 
         try:
             # Get Current dir
@@ -584,9 +610,9 @@ def importNeuroML(self, modelParameters):
             with redirect_stdout(sys.__stdout__):
                 # NetParams
                 filename = str(modelParameters["fileName"])
-               
+
                 json_fname = neuroml.convertNeuroML2(filename, compileMod=modelParameters["compileMod"])
-                   
+
             return self.loadModel(args=dict(
                 compileMod=True,
                 modFolder=os.path.dirname(json_fname),
@@ -605,7 +631,7 @@ def importNeuroML(self, modelParameters):
 
     def importLEMS(self, modelParameters):
         from netpyne_ui.helpers import neuroml
-       
+
 
         try:
             # Get Current dir
@@ -614,7 +640,7 @@ def importLEMS(self, modelParameters):
             with redirect_stdout(sys.__stdout__):
                 # NetParams
                 filename = str(modelParameters["fileName"])
-               
+
                 json_fname =  neuroml.convertLEMSSimulation(filename)
 
             return self.loadModel(args=dict(
@@ -789,10 +815,21 @@ def getPlotSettings(self, plot_name):
             return self.simConfig.analysis[plot_name]
         return {}
 
-    def getDirList(self, dir=None, onlyDirs=False, filterFiles=False):
-        # Get Current dir
+    def checkFileExists(self, path):
+        path = Path(path or '')
+        return path.exists()
+
+    def getFullPath(self, dir, subDir):
         if dir is None or dir == '':
-            dir = os.path.join(os.getcwd(), constants.NETPYNE_WORKDIR_PATH)
+            base = constants.NETPYNE_WORKDIR_PATH
+            if subDir:
+                base = os.path.join(base, subDir)
+            dir = os.path.join(os.getcwd(), base)
+        return dir
+
+    def getDirList(self, dir=None, onlyDirs=False, filterFiles=False, subDir=None):
+        # Get Current dir
+        dir = self.getFullPath(dir, subDir)
         dir_list = []
         file_list = []
         for f in sorted(os.listdir(str(dir)), key=str.lower):
@@ -810,6 +847,13 @@ def checkAvailablePlots(self):
     def getPlot(self, plotName, LFPflavour, theme='gui'):
         try:
             with redirect_stdout(sys.__stdout__):
+                availablePlots = self.checkAvailablePlots()
+                checkCondition = availablePlots.get(plotName.replace('iplot', 'plot'), False)
+
+                if checkCondition is False:
+                    logging.info("Plot " + plotName + " not available")
+                    return -1
+
                 args = self.getPlotSettings(plotName)
                 if LFPflavour:
                     args['plots'] = [LFPflavour]

requirements.txt

@@ -34,7 +34,7 @@ jupyterthemes==0.20.0
 kiwisolver==1.2.0
 lesscpy==0.14.0
 libNeuroML==0.4.0
-lfpykit==0.5
+lfpykit==0.5.1
 lxml==4.5.1
 Mako==1.1.0
 MarkupSafe==1.1.1
@@ -44,7 +44,7 @@ mistune==0.8.4
 multimethod==1.3
 nbconvert==5.6.1
 nbformat==5.0.6
-netpyne==1.0.3.1
+netpyne==1.0.4.1
 NEURON==8.2.2
 numpy==1.18.5
 oauthlib==3.0.1

setup.py

@@ -18,7 +18,7 @@
 
 setuptools.setup(
     name="netpyne_ui",
-    version="0.9.1",
+    version="1.0.0",
     url="https://github.com/MetaCell/NetPyNE-UI",
     author="MetaCell",
     author_email="info@metacell.us",
@@ -41,8 +41,8 @@
     ],
     install_requires=[
         'jupyter-geppetto>=1.0.0',
-        'NEURON>=8.0.2',
-        'netpyne>=1.0.3.1',
+        'NEURON>=8.2.2',
+        'netpyne>=1.0.4.1',
         'neuromllite==0.5.1',
         'pyNeuroML>=0.7.1',
         'sentry_sdk>=1.5.2',

webapp/Main.js

@@ -8,7 +8,7 @@ import { LoadingSpinner } from '@metacell/geppetto-meta-client/components';
 import { NetPyNE } from './components';
 import theme from './theme';
 import store from './redux/store';
-import '@metacell/geppetto-meta-ui/flex-layout/style/dark.scss';
+import '@metacell/geppetto-meta-ui/flex-layout/style/dark.css';
 
 global.GEPPETTO_CONFIGURATION = require('./GeppettoConfiguration.json');
 const { initGeppetto } = require('@metacell/geppetto-meta-client/GEPPETTO');

webapp/components/NetPyNE.js

@@ -12,7 +12,7 @@ import {
   LaunchDialog,
   TutorialObserver
 } from 'netpyne/components';
-
+import { loadModel } from '../redux/actions/general';
 
 const styles = ({ zIndex }) => ({
   root: {
@@ -41,15 +41,11 @@ const styles = ({ zIndex }) => ({
 });
 
 
-
 class NetPyNE extends React.Component {
   constructor (props) {
     super(props);
     this.openPythonCallDialog = this.openPythonCallDialog.bind(this);
-  }
-
-  componentDidUpdate() {
-    console.log('updated')
+    this.loaded = false;
   }
 
   componentDidMount () {
@@ -60,6 +56,35 @@ class NetPyNE extends React.Component {
     } = this.props;
 
     setDefaultWidgets();
+
+    // Listen messages
+    const loadFromEvent = (event) => {
+      // Here we would expect some cross-origin check, but we don't do anything more than load a model here
+      switch (event.data.type) {
+        case 'INIT_INSTANCE':
+          if (this.loaded) {
+            return;
+          }
+          this.loaded = true;
+          console.log('Netpyne is ready');
+          if (window !== window.parent) {
+            window.parent.postMessage({
+              type: 'APP_READY',
+            }, '*');
+          }
+          break;
+        case 'LOAD_RESOURCE':
+          // eslint-disable-next-line no-case-declarations
+          const resource = event.data.payload;
+          this.props.dispatchAction(loadModel(resource));
+          break;
+        default:
+          break;
+      }
+    };
+    // A message from the parent frame can specify the file to load
+    window.addEventListener('message', loadFromEvent);
+    // window.load = loadFromEvent
   }
 
   componentWillUnmount () {
@@ -80,8 +105,6 @@ class NetPyNE extends React.Component {
     }
   }
 
-
-
   render () {
     const { classes } = this.props;
 

webapp/components/definition/connectivity/NetPyNEConnectivityRule.js

@@ -198,12 +198,9 @@ export default class NetPyNEConnectivityRule extends React.Component {
                 `netParams.connParams['${this.props.name}']['synMech']`
               }
               fullWidth
+              multiple
               method="netpyne_geppetto.getAvailableSynMech"
-              postProcessItems={(pythonData, selected) => pythonData.map((name) => (
-                <MenuItem id={`${name}MenuItem`} key={name} value={name}>
-                  {name}
-                </MenuItem>
-              ))}
+              postProcessItems={this.postProcessMenuItems}
             />
           </NetPyNEField>
 

webapp/components/general/Dialog.js

@@ -26,21 +26,21 @@ const AboutContent = withStyles(styles)(({ classes }) => (
     <img width="250" src={logoNetpyne} />
     <Box m={1}>
       <Link variant="h5" style={{ display: 'block' }} href="https://github.com/MetaCell/NetPyNE-UI" target="_blank">
-        NetPyNE-UI v0.9.1
+        NetPyNE-UI v1.0.0
       </Link>
       <Link variant="h5" style={{ display: 'block' }} href="https://github.com/Neurosim-lab/netpyne" target="_blank">
-        NetPyNE v1.0.3.1
+        NetPyNE v1.0.4.1
       </Link>
       <Link variant="h5" style={{ display: 'block' }} href="https://www.neuron.yale.edu/neuron/" target="_blank">
-        NEURON v8.0.2
+        NEURON v8.2.2
       </Link>
     </Box>
 
     <Box m={1}>
       <Typography variant="body2" color={secondaryColor}>
         NetPyNE is a Python package to facilitate the development, simulation,
         parallelization, and analysis of biological neuronal networks using the
-        NEURON simulator. Checkout our
+        NEURON simulator. Check out our
         {' '}
         <Link href="https://elifesciences.org/articles/44494" target="_blank">
           eLife paper.