Merge pull request #120 from MetaCell/release/0.3.0

Release/0.3.0 download source file, cumulative fixes

Author: filippomc

.dockerignore

@@ -3,8 +3,8 @@
 *pyc
 /static/
 /dependencies/
-/webapp/build/
-/webapp/node_modules/
+# webapp/build/
+# /webapp/node_modules/
 /webapp/geppetto-client/
 .DS_Store
 *.egg-info/

README.md

@@ -7,6 +7,8 @@
 NWB Explorer is a web application that can be used by scientists to read, visualize and explore
 the content of NWB:N 2 files.
 
+![nwbexplorer](https://user-images.githubusercontent.com/39889/67516734-24c1e380-f66f-11e9-9fba-5151118f5e4d.gif)
+
 Learn more about the [Neurodata Without Borders](https://www.nwb.org/).
 
 ## Getting Started

nwb_explorer/api.py

@@ -79,11 +79,4 @@ def new_notebook(handler: IPythonHandler, path):
         if not os.path.exists(path):
             logging.info("Creating notebook {}".format(path))
             createNotebook(path)
-        return handler.render_template('notebook.html',
-                                       notebook_path=path,
-                                       notebook_name=path.split('/')[-1],
-                                       kill_kernel=False,
-                                       mathjax_url=handler.mathjax_url,
-                                       mathjax_config=handler.mathjax_config,
-                                       get_custom_frontend_exporters=get_custom_frontend_exporters
-                                       )
+        handler.redirect('notebooks/' + path)

nwb_explorer/nwb_model_interpreter/nwb_model_interpreter.py

@@ -26,8 +26,9 @@ def assign_name_to_type(pynwb_obj):
 class NWBModelInterpreter(ModelInterpreter):
 
     def __init__(self, nwb_file_name):
+
         logging.info(f'Creating a Model Interpreter for {nwb_file_name}')
-        self.nwb_file_name = nwb_file_name
+        self.nwb_file_name = nwb_file_name if isinstance(nwb_file_name, str) else 'in-memory file'
         self.nwb_reader = NWBReader(nwb_file_name)
         self.library = GeppettoLibrary(name='nwbfile', id='nwbfile')
 
@@ -45,7 +46,7 @@ def create_model(self):
 
         geppetto_model.libraries.append(self.library)
 
-        obj_type = ImportType(autoresolve=True)
+        obj_type = ImportType(autoresolve=True, url=self.nwb_file_name, id="nwbfile", name='nwbfile')
         self.library.types.append(obj_type)
         obj_variable = Variable(id='nwbfile', name='nwbfile', types=(obj_type,))
         geppetto_model.variables.append(obj_variable)
@@ -58,7 +59,7 @@ def importType(self, url, type_name, library, geppetto_model_access: GeppettoMod
         mapper = GenericCompositeMapper(model_factory, library)
         # build compositeTypes for pynwb objects
         root_type = mapper.create_type(self.get_nwbfile(), type_name=type_name, type_id=type_name)
-        if isinstance(self.nwb_file_name, str) and url == 'nwbfile':
+        if isinstance(self.nwb_file_name, str) and type_name == 'nwbfile':
             from nwb_explorer.nwb_data_manager import CACHE_DIRNAME
             root_type.variables.append(
                 model_factory.create_url_variable(

setup.py

@@ -16,7 +16,7 @@
 
 setuptools.setup(
     name="nwb_explorer",
-    version="0.2",
+    version="0.3",
     url="https://github.com/tarelli/nwb-explorer",
     author="MetaCell",
     author_email="info@metacell.us",

webapp/components/App.js

@@ -36,11 +36,11 @@ export default class App extends React.Component{
     const { loadNWBFile, loadNotebook, notebookReady, nwbFileLoaded, raiseError } = this.props;
     self = this;
 
-    const cookieName = 'nwbloadurl'
+    const cookieName = 'nwbloadurl';
     const nwbCookie = document.cookie.split(';').find(cookie => cookie.includes(cookieName))
     if (nwbCookie) {
-      const [_, nwbFileUrl] = nwbCookie.replace(/"/g, '').split("=")
-      if (nwbFileUrl && document.location.href.includes("nwbexplorer.opensourcebrain.org")) {
+      const [_, nwbFileUrl] = nwbCookie.replace(/"/g, '').split("=");
+      if (nwbFileUrl) {
         document.cookie = `${cookieName}= ; path=/`;
         loadNWBFile(nwbFileUrl);
       }

webapp/middleware/nwbMiddleware.js

@@ -16,12 +16,12 @@ function handleShowWidget (store, next, action) {
   if (action.data.type === 'TimeSeries') { // Instances.getInstance(path).getType().wrappedObj.name
     store.dispatch(updateDetailsWidget(action.data.instancePath));
     return handlePlotTimeseries(store, next, action);
-  }
-  if (action.data.type === 'ImageSeries') { // Instances.getInstance(path).getType().wrappedObj.name
+  } else if (action.data.type === 'ImageSeries') { // Instances.getInstance(path).getType().wrappedObj.name
     store.dispatch(updateDetailsWidget(action.data.instancePath));
     return handleImportTimestamps(store, next, action);
+  } else {
+    return next(action);
   }
-  return next(action);
 }
 
 function handleImportTimestamps (store, next, action) {
@@ -75,11 +75,13 @@ function handlePlotTimeseries (store, next, action) {
 }
 
 const nwbMiddleware = store => next => action => {
-  next(action);
+  
   switch (action.type) {
 
   case LOAD_NWB_FILE:
+    next(action);
     Project.loadFromURL(action.data.nwbFileUrl);
+    
     GEPPETTO.on('jupyter_geppetto_extension_ready', data => { // It's triggered once
 
       console.log("Initializing Python extension");
@@ -95,28 +97,33 @@ const nwbMiddleware = store => next => action => {
 
 
   case LOAD_NWB_FILE_IN_NOTEBOOK:
+    next(action);
     nwbFileService.loadNWBFileInNotebook(store.getState().nwbfile.nwbFileUrl).then(
       () => store.dispatch(loadedNWBFileInNotebook)
     );
+    
     break;
 
   case UNLOAD_NWB_FILE_IN_NOTEBOOK:
+    next(action);
     Utils.execPythonMessage('del nwbfile');
+    
     break;
 
   case NOTEBOOK_READY:
+    next(action);
     // FIXME for some reason the callback for python messages is not being always called
     Utils.execPythonMessage('from nwb_explorer.nwb_main import main');
     store.dispatch(loadNWBFileInNotebook);
-    
+
     break;
 
   case UPDATE_WIDGET:
   case ADD_WIDGET:
-    return handleShowWidget(store, next, action);
-  
   case ADD_PLOT_TO_EXISTING_WIDGET:
-    return handlePlotTimeseries(store, next, action)
+    return handleShowWidget(store, next, action);
+    
+  default: next(action);
   }
 
 

webapp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nwb-explorer",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "description": "NWB Explorer is an application that can be used by scientists to read, visualize and explore the content of NWB 2 files.",
   "repository": "https://github.com/MetaCell/geppetto-nwbexplorer",
   "license": "MIT",

webapp/services/NotebookService.js

@@ -7,7 +7,7 @@ export function getNotebookPath () {
   if (nwbFileParam){
     return "notebook?path=" + nwbFileParam.split('/').slice(-1) + '.ipynb';
   }
-  return "notebook?path=notebook.ipynb";
+  return "notebook?path=nwbnotebook.ipynb";
 }
 
 var console = null;