Merge pull request #808 from MetaCell/feature/NETPYNE-209

Fix OSB integration

Author: ddelpiano

Dockerfile

@@ -11,6 +11,11 @@ RUN yarn install  --network-timeout 1000000000
 COPY webapp .
 RUN yarn build-dev
 
+### Download on a separate stage to run in parallel with buildkit
+FROM jupyter/base-notebook:hub-1.5.0 as downloads
+USER root
+RUN wget --no-check-certificate -O /nyhead.mat https://www.parralab.org/nyhead/sa_nyhead.mat
+
 ###
 FROM jupyter/base-notebook:hub-1.5.0
 ENV NB_UID=jovyan
@@ -31,22 +36,29 @@ COPY  --chown=1000:1000 requirements.txt requirements.txt
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
     pip install -r requirements.txt --prefer-binary
 
-COPY . .
-COPY --from=jsbuild --chown=1000:1000 $FOLDER/webapp/build webapp/build
 
 # ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default
 # and thus removes the frame ancestor cors settings
 RUN rm -f ~/.jupyter/*.json
 RUN chown $NB_UID .
 RUN chown $NB_UID /opt
 RUN rm -Rf workspace
-
-USER $NB_UID
-
 # sym link workspace pvc to $FOLDER
 RUN mkdir -p /opt/workspace
 RUN mkdir -p /opt/user
 
+COPY netpyne_ui netpyne_ui
+COPY utilities utilities
+COPY setup.py .
+COPY  tests tests
+COPY NetPyNE-UI .
+COPY README.rst .
+COPY requirements-test.txt .
+
+USER $NB_UID
+
+
+
 
 ENV NEURON_HOME=/opt/conda
 
@@ -61,15 +73,17 @@ RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
 ARG BUILD_ARGS=""
 ARG WORKSPACE_VERSION=master
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
-  python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION
+  python utilities/install.py ${BUILD_ARGS} --workspace $WORKSPACE_VERSION --npm-skip
 
 
 RUN mv workspace /opt/workspace/tutorials
 RUN chown -R $NB_UID /opt/workspace/tutorials
 RUN ln -s /opt/workspace workspace
 
 RUN jupyter labextension disable @jupyterlab/hub-extension
-RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat
+
+COPY --from=downloads --chown=1000:1000 /nyhead.mat $NP_LFPYKIT_HEAD_FILE
+COPY --from=jsbuild --chown=1000:1000 $FOLDER/webapp/build webapp/build
 
 USER $NB_UID
 

webapp/components/NetPyNE.js

@@ -12,7 +12,7 @@ import {
   LaunchDialog,
   TutorialObserver,
 } from 'netpyne/components';
-import { loadModel, openDialog } from '../redux/actions/general';
+import { openDialog } from '../redux/actions/general';
 // import { execPythonMessage } from './general/GeppettoJupyterUtils';
 import { replayAll } from './general/CommandRecorder';
 
@@ -47,7 +47,6 @@ class NetPyNE extends React.Component {
   constructor (props) {
     super(props);
     this.openPythonCallDialog = this.openPythonCallDialog.bind(this);
-    this.loaded = false;
     this.kernelRestartState = {
       state: "idle",
       kernelID: undefined,
@@ -64,33 +63,7 @@ class NetPyNE extends React.Component {
 
     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-UI component 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);
+
 
     // Logic for kernel reinit
     const handleKernelRestart = ({ detail: { kernel, type } }) => {

webapp/redux/middleware/middleware.js

@@ -26,12 +26,13 @@ import {
   addInstancesToCanvas,
   openConfirmationDialog,
   registerModelPath,
+  loadModel,
   LOAD_MODEL
 } from '../actions/general';
 import { OPEN_BACKEND_ERROR_DIALOG, CLOSE_BACKEND_ERROR_DIALOG, openBackendErrorDialog } from '../actions/errors';
 import { closeDrawerDialogBox } from '../actions/drawer';
 import Utils from '../../Utils';
-import { downloadJsonResponse, downloadPythonResponse } from './utils';
+import { downloadJsonResponse, downloadPythonResponse, initParentFrameMessaging } from './utils';
 import * as Constants from '../../constants';
 import { ADD_EXPERIMENT, REMOVE_EXPERIMENT } from '../actions/experiments';
 
@@ -249,6 +250,36 @@ export default (store) => (next) => (action) => {
 
   }
 
+  
+  /**
+   * Notify parent frame that the app is ready
+   * Used in Open Source Brain integration
+   */
+  function initParentFrameMessaging () {
+    if (window !== window.parent) {
+      window.parent.postMessage({
+        type: 'APP_READY',
+      }, '*');
+    
+
+    // Listen messages from the parent frame (Open Source Brain integration)
+      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 'LOAD_RESOURCE':
+            // eslint-disable-next-line no-case-declarations
+            const resource = event.data.payload;
+            store.dispatch(loadModel(resource));
+            break;
+          default:
+            break;
+        }
+      };
+      // A message from the parent frame can specify the file to load
+      window.addEventListener('message', loadFromEvent);
+    }
+  }
+
   switch (action.type) {
     case GeppettoActions.layoutActions.SET_WIDGETS: {
       if (Object.values(action.data).length == 1) {
@@ -291,6 +322,9 @@ export default (store) => (next) => (action) => {
           getExperiments()
         });
       Utils.execPythonMessage(`netpyne_geppetto.saveToIndexFile(None, "${Constants.KERNEL_HANDLING.tmpModelPath}", True, True)`, ()=>{}, false);
+      
+
+      initParentFrameMessaging();
 
       setTimeout(() => {
         if (!responded) {
@@ -299,6 +333,8 @@ export default (store) => (next) => (action) => {
             .then(() => window.location.reload());
         }
       }, TIMEOUT);
+
+      
       break;
     }
     case OPEN_BACKEND_ERROR_DIALOG:
@@ -529,3 +565,4 @@ export default (store) => (next) => (action) => {
     }
   }
 };
+