MetaCell · ddelpiano · Jan 24, 2024 · Nov 7, 2023 · Nov 8, 2023 · Nov 8, 2023
diff --git a/webapp/components/NetPyNE.js b/webapp/components/NetPyNE.js
@@ -10,9 +10,11 @@ import {
   Dialog,
   ConfirmationDialog,
   LaunchDialog,
-  TutorialObserver
+  TutorialObserver,
 } from 'netpyne/components';
-import { loadModel } from '../redux/actions/general';
+import { loadModel, openDialog } from '../redux/actions/general';
+// import { execPythonMessage } from './general/GeppettoJupyterUtils';
+import { replayAll } from './general/CommandRecorder';
 
 const styles = ({ zIndex }) => ({
   root: {
@@ -46,6 +48,11 @@ class NetPyNE extends React.Component {
     super(props);
     this.openPythonCallDialog = this.openPythonCallDialog.bind(this);
     this.loaded = false;
+    this.kernelRestartState = {
+      state: "idle",
+      kernelID: undefined,
+      crashLoop: false
+    }
   }
 
   componentDidMount () {
@@ -66,7 +73,7 @@ class NetPyNE extends React.Component {
             return;
           }
           this.loaded = true;
-          console.log('Netpyne is ready');
+          console.log('NetPyNE-UI component is ready');
           if (window !== window.parent) {
             window.parent.postMessage({
               type: 'APP_READY',
@@ -84,7 +91,107 @@ class NetPyNE extends React.Component {
     };
     // A message from the parent frame can specify the file to load
     window.addEventListener('message', loadFromEvent);
-    // window.load = loadFromEvent
+
+    // Logic for kernel reinit
+    const handleKernelRestart = ({ detail: { kernel, type } }) => {
+      switch (this.kernelRestartState.state) {
+        case "restarting":
+          if (type === "kernel_ready" || type === "kernel_autorestarting") {
+            console.log("Replaying all commands since the beginning of the session")
+            replayAll(this.kernelRestartState.kernelID)
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: "idle",
+              kernelID: undefined,
+            }
+          }
+        case "idle":
+          if (type === "kernel_connected") {
+            console.log("Kernel is connecting/starting, being init")
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: "init",
+              kernelID: kernel.id
+            }
+          }
+          else if (type === "kernel_autorestarting") {
+            console.log("Kernel restart event caught, trying to re-init the current model")
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: "restarting",
+              kernelID: kernel.id
+            }
+            if (!this.kernelRestartState.crashLoop) {
+              this.props.dispatchAction(openDialog({
+                title: "Kernel restart",
+                message: "An action occured that made the kernel restart. We are reloading your model and all the actions you applied on it."
+              }))
+            }
+          }
+          else if (type === "kernel_restarting") {
+            console.log("Kernel restart, perhaps it's a special restart?")
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: "special_restart",
+              kernelID: kernel.id
+            }
+          }
+        case "init":
+          if (type === "kernel_ready") {
+            console.log("Kernel properly initialized")
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: "idle",
+              kernelID: undefined,
+            }
+          }
+        case "special_restart":
+          if (type == "kernel_autorestarting") {
+            console.log("Kernel autorestart after a start, we might not have the ready event, we force it then")
+            replayAll(this.kernelRestartState.kernelID)
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: 'restarting',
+              kernelID: kernel.id,
+            }
+          } else {
+            console.log("Regular restart detected")
+            this.kernelRestartState = {
+              ...this.kernelRestartState,
+              state: 'idle',
+              kernelID: undefined,
+            }
+          }
+      }
+    }
+    window.addEventListener('kernelstatus', handleKernelRestart)
+
+    // Dedicated code to handle crash loops
+    const kernelRestartLoopHandler = ( ) => {
+      if (!this.kernelRestartState.crashLoop) {
+        this.props.dispatchAction(openDialog({
+          title: "Kernel restart loop stabilization",
+          message: "One of your actions triggered a kernel restart loop. We are trying to identify the faulty command and to restore your model until this point. Close this window and wait for the kernel stabilization notification."
+        }))
+      } else {
+        clearTimeout(this.kernelRestartState.crashLoop)
+      }
+      const taskID = setTimeout((_this) => {
+        this.props.dispatchAction(openDialog({
+          title: "Kernel restart loop stabilized",
+          message: "The kernel is now stabilized."
+        }));
+        this.kernelRestartState = {
+          ...this.kernelRestartState,
+          crashLoop: false
+        }
+      }, 8000, this)
+      this.kernelRestartState = {
+        ...this.kernelRestartState,
+        crashLoop: taskID
+      }
+    }
+    window.addEventListener('kernelRestartLoop', kernelRestartLoopHandler)
   }
 
   componentWillUnmount () {
@@ -115,6 +222,9 @@ class NetPyNE extends React.Component {
           <div className={classes.container}>
             <div className={classes.topbar}>
               <Topbar />
+        {/* <button onClick={() => {
+          execPythonMessage("utils.convertToJS(netpyne_geppetto.importCellTemplate(utils.convertToPython('{\"cellArgs\":{},\"fileName\":\"/home/vince/git-repository/metacell/NetPyNE-UI/workspace/cells/FScell.hoc\",\"cellName\":\"FScell\",\"label\":\"CellType1\",\"modFolder\":\"/home/vince/git-repository/metacell/NetPyNE-UI/workspace/mod\",\"importSynMechs\":false,\"compileMod\":false}')))")
+        }}>CRASH ME</button> */}
             </div>
             <Box p={1} flex={1} display="flex" alignItems="stretch">
               <Grid container spacing={1} className={classes.content} alignItems="stretch">

diff --git a/webapp/components/general/CommandRecorder.js b/webapp/components/general/CommandRecorder.js
@@ -0,0 +1,103 @@
+import { KERNEL_HANDLING } from '../../constants';
+import { store } from '../../redux/actiondomainStore'
+import { recordCommand, dropLastCommand, dropFromIndex } from '../../redux/actions/actiondomain';
+import { execPythonMessage, execPythonMessageWithoutRecording } from './GeppettoJupyterUtils';
+
+
+const registerKernelListeners = () => {
+  try {
+    if(IPython.notebook.kernel == null) {
+      console.warn("Kernel not initialized. Waiting to register kernel event listeners");
+      setTimeout(registerKernelListeners, 500);
+      return;
+    }
+  } catch (error) {
+    console.warn("IPython not initialized.  Waiting to register kernel event listeners");
+    setTimeout(registerKernelListeners, 500);
+    return
+  }
+
+  const notebook = IPython.notebook;
+  const handleKernelStatusChange = (event, data) => {
+    const kernelStatusEvent = new CustomEvent("kernelstatus", {
+        detail: {
+          "type": event.type,
+          ...data
+        },
+    });
+    window.dispatchEvent(kernelStatusEvent);
+  };
+
+  const handleExecutionRequest = (event, data) => {
+    if (data.content.netpyne_ui_triggered) {
+      return
+    }
+    const { kernel, content } = data;
+    record(kernel.id, content.code);
+  }
+
+  // Kernel lifecycle requests
+  notebook.events.on('kernel_created.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_reconnecting.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_connected.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_starting.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_restarting.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_autorestarting.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_interrupting.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_disconnected.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_ready.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_killed.Kernel', handleKernelStatusChange);
+  notebook.events.on('kernel_dead.Kernel', handleKernelStatusChange);
+
+  // Execution requests
+  notebook.events.on('execution_request.Kernel', handleExecutionRequest);
+}
+registerKernelListeners();
+
+
+const record = (kernelID, command) => {
+  store.dispatch(recordCommand(kernelID, command))
+}
+
+const TIMEFRAME = 10 * 1000; // 10s
+let lastReplayTime = 0
+
+const getCommands = (kernelID) => {
+  return [
+    "from jupyter_geppetto import jupyter_geppetto",
+    "from jupyter_geppetto import utils",
+    "from netpyne_ui.netpyne_geppetto import netpyne_geppetto",
+    "netpyne_geppetto.deleteModel({})",
+    `netpyne_geppetto.loadFromIndexFile("${KERNEL_HANDLING.tmpModelPath}")`,
+    ...store.getState()[kernelID]
+  ]
+}
+
+const replayAll = (kernelID, fromRec = false) => {
+  const currentTimestamp = Date.now();
+  const commands = getCommands(kernelID);
+
+  if (!fromRec && currentTimestamp - lastReplayTime < TIMEFRAME) {
+    const restartLoop = new CustomEvent("kernelRestartLoop", {
+        detail: {
+          "kernel": kernelID,
+          "state": "looping"
+        }
+    });
+    window.dispatchEvent(restartLoop);
+    store.dispatch(dropLastCommand(kernelID))
+    replayAll(kernelID, true)
+    return
+  }
+
+  const lastCommand = commands.pop()  // we drop the last command which is probably the faulty one
+  const script = commands.join('\n')
+  console.log("Playing", script)
+  console.log("Skipping last command", lastCommand)
+  lastReplayTime = currentTimestamp
+  execPythonMessageWithoutRecording(script).then(() => {
+    store.dispatch(dropLastCommand(kernelID))
+  })
+}
+
+export { record, replayAll }
diff --git a/webapp/components/general/Dialog.js b/webapp/components/general/Dialog.js
@@ -1,14 +1,7 @@
 import React from 'react';
-import Button from '@material-ui/core/Button';
 import MuiDialog from '@material-ui/core/Dialog';
-import DialogActions from '@material-ui/core/DialogActions';
-import DialogContent from '@material-ui/core/DialogContent';
-import Typography from '@material-ui/core/Typography';
-import DialogTitle from '@material-ui/core/DialogTitle';
-import Paper from '@material-ui/core/Paper';
-import Box from '@material-ui/core/Box';
-import Link from '@material-ui/core/Link';
-import Icon from '@material-ui/core/Icon';
+import { Button,DialogActions, DialogContent, DialogTitle, DialogContentText } from '@material-ui/core';
+import { Typography, Paper, Box, Link, Icon } from '@material-ui/core';
 import { withStyles } from '@material-ui/core/styles';
 import { secondaryColor, bgLight } from '../../theme';
 import logoNetpyne from '../../static/netpyne-logo_white.png';
@@ -135,18 +128,31 @@ const ContributeContent = withStyles(styles)(({ classes }) => (
   </Paper>
 ));
 
+
+const titleContentMapping = {
+  Contribute: <ContributeContent />,
+  About: <AboutContent />
+}
+
 export default function Dialog ({
   open,
   title,
   message,
   handleClose,
 }) {
+  const selectMessageContent = () => {
+    if (title in titleContentMapping) {
+      return titleContentMapping[title]
+    }
+    return <DialogContentText>{message}</DialogContentText>
+  }
   return (
     <div>
       <MuiDialog fullWidth maxWidth="sm" open={open} onClose={handleClose}>
         <DialogTitle>{title}</DialogTitle>
         <DialogContent>
-          {title === 'Contribute' ? <ContributeContent /> : <AboutContent />}
+          {/* {title === 'Contribute' ? <ContributeContent /> : <AboutContent />} */}
+          {selectMessageContent()}
         </DialogContent>
         <DialogActions>
           <Button onClick={handleClose} color="primary" autoFocus>

diff --git a/webapp/components/general/GeppettoJupyterUtils.js b/webapp/components/general/GeppettoJupyterUtils.js
@@ -1,3 +1,6 @@
+import { record as recordCommand } from './CommandRecorder';
+
+
 const handle_output = function (data) {
   // data is the object passed to the callback from the kernel execution
   switch (data.msg_type) {
@@ -29,9 +32,23 @@ const handle_output = function (data) {
   }
 };
 
-const execPythonMessage = function (command, callback = handle_output) {
+const execPythonMessage = function (command, callback = handle_output, record = true) {
   const { kernel } = IPython.notebook;
-  const messageID = kernel.execute(command, { iopub: { output: callback } }, { silent: false, stop_on_error: true, store_history: true });
+  if (record) {
+    recordCommand(kernel.id, command)
+  }
+  const messageID = kernel.execute(
+    command,
+    {
+      iopub: { output: callback }
+    },
+    {
+      silent: false,
+      stop_on_error: true,
+      store_history: true,
+      netpyne_ui_triggered: true
+    });
+
 
   return new Promise((resolve, reject) => GEPPETTO.on(GEPPETTO.Events.Receive_Python_Message, (data) => {
     if (data.data.id == messageID) {
@@ -40,11 +57,15 @@ const execPythonMessage = function (command, callback = handle_output) {
   }));
 };
 
+const execPythonMessageWithoutRecording = function (command, callback = handle_output) {
+  return execPythonMessage(command, callback, false)
+}
+
 const addslashes = function (str) {
   return (str + '').replace(/[\\"']/g, '\\$&').replace(/\u0000/g, '\\0');
 }
 
-const evalPythonMessage = function (command, parameters, parse = true) {
+const evalPythonMessage = function (command, parameters, parse = true, record = true) {
   let parametersString = '';
   if (parameters) {
     if (parameters.length > 0) {
@@ -58,7 +79,7 @@ const evalPythonMessage = function (command, parameters, parse = true) {
   if (parse) {
     finalCommand = `utils.convertToJS(${finalCommand})`;
   }
-  return execPythonMessage(finalCommand, handle_output);
+  return execPythonMessage(finalCommand, handle_output, record);
 };
 
-export { execPythonMessage, evalPythonMessage };
+export { execPythonMessage, evalPythonMessage, execPythonMessageWithoutRecording };
diff --git a/webapp/components/topbar/dialogs/ActionDialog.js b/webapp/components/topbar/dialogs/ActionDialog.js
@@ -46,10 +46,13 @@ class ActionDialog extends React.Component {
         }
       }
     }
-    this.setState({ hide: true });
     if (this.props.onAction) {
       this.props.onAction();
     }
+    this.setState({ hide: true });
+    if (this.props.onRequestClose) {
+      this.props.onRequestClose();
+    }
   };
 
   clearErrorDialogBox () {

diff --git a/webapp/components/topbar/dialogs/ActionValidationDialog.js b/webapp/components/topbar/dialogs/ActionValidationDialog.js
@@ -46,6 +46,9 @@ const ActionValidationDialog = (props) => {
     if (props.onAction) {
       props.onAction()
     }
+    if (props.onRequestClose) {
+      props.onRequestClose()
+    }
   }
 
   const clearErrorDialogBox = () => {