Merge pull request #639 from MetaCell/release/0.9.0

Release/0.9.0

Author: ddelpiano

Dockerfile

@@ -12,9 +12,7 @@ COPY webapp/ .
 RUN yarn build-dev
 
 
-RUN mv node_modules/@metacell .
 RUN rm -Rf node_modules/*
-RUN mv @metacell node_modules
 
 ###
 FROM jupyter/base-notebook:hub-1.5.0

netpyne_ui/api.py

@@ -10,6 +10,7 @@
 from notebook.base.handlers import IPythonHandler
 from netpyne_ui.constants import ALLOWED_EXTENSIONS, UPLOAD_FOLDER_PATH
 
+
 def allowed_file(filename, allowed_extensions=ALLOWED_EXTENSIONS):
     return '.' in filename and \
            filename.rsplit('.', 1)[1].lower() in allowed_extensions
@@ -43,6 +44,23 @@ def get_file_paths(handler):
     return file_paths
 
 
+def is_within_directory(directory, target):
+    abs_directory = os.path.abspath(directory)
+    abs_target = os.path.abspath(target)
+
+    prefix = os.path.commonprefix([abs_directory, abs_target])
+
+    return prefix == abs_directory
+
+
+def safe_extract_tar(tar, path=".", members=None, *, numeric_owner=False):
+    for member in tar.getmembers():
+        member_path = os.path.join(path, member.name)
+        if not is_within_directory(path, member_path):
+            raise Exception("Attempted Path Traversal in Tar File")
+    tar.extractall(path, members, numeric_owner=numeric_owner)
+
+
 class NetPyNEController:  # pytest: no cover
 
     @post('/uploads')
@@ -74,7 +92,7 @@ def uploads(handler: IPythonHandler):
 
                 elif filename.endswith('.tar.gz'):
                     with tarfile.open(file_path, mode='r:gz') as tar:
-                        tar.extractall(UPLOAD_FOLDER_PATH)
+                        safe_extract_tar(tar, UPLOAD_FOLDER_PATH)
 
                 elif filename.endswith('.gz'):
                     with gzip.open(file_path, "rb") as gz, open(file_path.replace('.gz', ''), 'wb') as ff:

netpyne_ui/netpyne_geppetto.py

@@ -192,6 +192,8 @@ def instantiateNetPyNEModelInGeppetto(self, args):
         try:
             with redirect_stdout(sys.__stdout__):
                 if not args.get("usePrevInst", False):
+                    if self.doIhaveInstOrSimData()['haveInstance']:
+                        sim.clearAll()
                     netpyne_model = self.instantiateNetPyNEModel()
                     self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
 
@@ -259,7 +261,7 @@ def simulate_single_model(self, experiment: model.Experiment = None, use_prev_in
                 netpyne_model = self.instantiateNetPyNEModel()
 
                 self.geppetto_model = self.model_interpreter.getGeppettoModel(netpyne_model)
-            
+
             simulations.run()
 
             if self.geppetto_model:
@@ -374,7 +376,7 @@ def _prepare_simulation_files(self, experiment: model.Experiment = None, use_pre
 
     def _prepare_batch_files(self, experiment: model.Experiment) -> str:
         """Creates template files and netpyne model files in the experiment folder.
-        
+
         Only for an experiment consisting of many trials.
 
         :param experiment: given experiment

requirements.txt

@@ -23,7 +23,7 @@ jedi==0.17.0
 Jinja2==2.11.2
 jsonpickle==2.1.0
 jsonschema==3.2.0
-jupyter_geppetto==1.1.4
+jupyter_geppetto==1.1.5
 jupyter-client==7.0.6
 jupyter-core==4.9.1
 jupyter-server==1.11.2
@@ -43,10 +43,11 @@ multimethod==1.3
 nbconvert==5.6.1
 nbformat==5.0.6
 neuromllite==0.1.9
-netpyne==1.0.2.1
+netpyne==1.0.3
 NEURON==8.0.2
 numpy==1.18.5
 oauthlib==3.0.1
+optuna==2.10.1
 ordered-set==4.0.2
 pamela==1.0.0
 pandas==0.23.4

setup.py

@@ -15,7 +15,7 @@
 
 setuptools.setup(
     name="netpyne_ui",
-    version="0.8.1",
+    version="0.9.0",
     url="https://github.com/MetaCell/NetPyNE-UI",
     author="MetaCell",
     author_email="info@metacell.us",

tests/frontend/e2e/package-lock.json

@@ -4051,10 +4051,10 @@ minimatch@^3.0.4:
   dependencies:
     brace-expansion "^1.1.7"
 
-minimist@^1.1.1, minimist@^1.2.5:
-  version "1.2.5"
-  resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.5.tgz#67d66014b66a6a8aaa0c083c5fd58df4e4e97602"
-  integrity sha512-FM9nNUYrRBAELZQT3xeZQ7fmMOBg6nWNmJKTcgsJeaLstP/UODVpGsr5OhXhhXg6f+qtJ8uiZ+PUxkDWcgIXLw==
+minimist@^1.1.1, minimist@^1.2.0, minimist@^1.2.5:
+  version "1.2.6"
+  resolved "https://registry.yarnpkg.com/minimist/-/minimist-1.2.6.tgz#8637a5b759ea0d6e98702cfb3a9283323c93af44"
+  integrity sha512-Jsjnk4bw3YJqYzbdyBiNsPWHPfO++UGG749Cxs6peCu5Xg4nrena6OVxOYxrQTqww0Jmwt+Ref8rggumkTLz9Q==
 
 minimist@^1.2.0:
   version "1.2.7"

tests/frontend/e2e/yarn.lock

@@ -116,12 +116,12 @@ def main(netpyne_branch, workspace_branch, geppetto_branch=None, skipNpm=False,
         execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, META_DIR, JUPYTER_DIR))
         # installing core dependencies
         execute(cmd=['pip', 'install', '-e', '.'], cwd=ROOT_DIR)
-    else:
-        # install requirements
         if netpyne_branch and netpyne_branch != 'master':
           cprint("Installing netpyne")
           clone(repository=NETPYNE, branch_or_tag=netpyne_branch)
           execute(cmd=['pip', 'install', '-e', '.'], cwd=os.path.join(DEPS_DIR, NETPYNE_DIR))
+    else:
+        # install requirements
         cprint("Installing UI python package...")
         execute(cmd=['pip', 'install', '-e', '.', '--no-deps'], cwd=ROOT_DIR)
 

utilities/install.py

@@ -13,15 +13,19 @@ import '@metacell/geppetto-meta-ui/flex-layout/style/dark.scss';
 global.GEPPETTO_CONFIGURATION = require('./GeppettoConfiguration.json');
 const { initGeppetto } = require('@metacell/geppetto-meta-client/GEPPETTO');
 
-Sentry.init({
-  dsn: 'https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6',
-  integrations: [
-    new CaptureConsole({
-      levels: ['error'],
-    }),
-  ],
-  tracesSampleRate: 1.0,
-});
+if (process.env.NODE_ENV == 'production')
+{
+  Sentry.init({
+    dsn: 'https://d8bf7e40eec34cb9891f6dd8207b5e83@sentry.metacell.us/6',
+    integrations: [
+      new CaptureConsole({
+        levels: ['error'],
+      }),
+    ],
+    tracesSampleRate: 1.0,
+  });
+}
+
 
 initGeppetto();
 require('./css/netpyne.less');

webapp/Main.js

@@ -25,7 +25,8 @@ const Utils = {
   },
 
   captureSentryException (e) {
-    Sentry.captureException(e);
+    if (process.env.NODE_ENV == 'production')
+      Sentry.captureException(e);
     console.error(e);
   },