Dependabot suggested dependency upgrades

frontend/v1/package.json

@@ -1,6 +1,6 @@
 {
   "name": "chimbuko-vis",
-  "version": "3.0.0",
+  "version": "3.0.1",
   "description": "Front-end package of Chimbuko visualization",
   "main": "index.js",
   "scripts": {
@@ -9,7 +9,7 @@
     "dev-build": "webpack --mode development --progress --config webpack.config.js",
     "watch": "webpack --mode development --progress --config webpack.config.js --watch"
   },
-  "author": "Sungsoo Ha, Wei Xu",
+  "author": "David Dakota Blair, Sungsoo Ha, Wei Xu",
   "license": "ISC",
   "devDependencies": {
     "babel-core": "^6.26.3",
@@ -26,16 +26,19 @@
     "webpack-cli": "^5.1.4"
   },
   "dependencies": {
+    "@babel/runtime": "^7.27.6",
     "@material-ui/core": "^4.4.0",
     "@material-ui/icons": "^4.2.1",
     "@material-ui/lab": "^4.0.0-alpha.29",
     "@material-ui/styles": "^4.3.3",
     "axios": "^1.8.4",
+    "brace-expansion": "^1.1.12",
     "chart.js": "^2.9.4",
     "chartjs-plugin-streaming": "1.8.0",
     "chartjs-plugin-zoom": "^0.7.7",
     "clsx": "^1.0.4",
     "d3": "^5.12.0",
+    "form-data": "^4.0.4",
     "history": "^4.9.0",
     "moment": "^2.29.4",
     "ncp": "^2.0.0",

manager.py

@@ -2,10 +2,11 @@
 from gevent import monkey
 monkey.patch_all()
 
-import types
+import collections
+import os
 import subprocess
 import sys
-import os
+import types
 
 # monkey patch flask to support old version of flask_script
 import flask
@@ -16,7 +17,9 @@
 _compat.text_type = str
 sys.modules[module_name] = _compat
 setattr(flask, '_compat', _compat)
-flask._request_ctx_stack = None
+mock_request_ctx_stack = collections.namedtuple("mock", ["top"])
+mock_request_ctx_stack.top = collections.namedtuple("top", ["app"])
+flask._request_ctx_stack = mock_request_ctx_stack
 
 from flask_script import Manager, Command, Server as _Server, Option
 

requirements.txt

@@ -11,8 +11,8 @@ Cython==3.0.4
 dnspython==2.6.1
 flask==3.0.3
 Flask-Script==2.0.6
-Flask-SocketIO==2.9.6
-Flask-SQLAlchemy==2.5.1
+Flask-SocketIO==5.5.1
+Flask-SQLAlchemy==3.1.1
 flit_core==3.9.0
 gevent==24.2.1
 greenlet==2.0.2
@@ -25,15 +25,15 @@ MarkupSafe==2.1.5
 pkgconfig==1.5.5
 pybind11==2.13.4
 pycparser==2.21
-python-engineio==4.10.1
-python-socketio==5.11.4
+python-engineio==4.12.2
+python-socketio==5.13.0
 pytz==2023.3
 redis==4.5.4
-requests==2.32.3
+requests==2.32.4
 runstats==1.8.0
 six==1.16.0
-SQLAlchemy==1.4.45
-urllib3==1.26.19
+SQLAlchemy==2.0.41
+urllib3==2.2.3
 vine==5.1.0
 werkzeug==3.0.6
 zipp==3.20

server/server.py

@@ -1,3 +1,6 @@
+import json
+import os
+
 from flask import (
     Blueprint,
     Response,
@@ -13,6 +16,15 @@
 main = Blueprint('main', __name__)
 
 
+@main.route('/build')
+def build():
+    with open("./frontend/v1/package.json") as f:
+        npm_package = json.load(f)
+    return jsonify({
+        "npm_package_version": npm_package["version"]
+    })
+
+
 @main.before_app_request
 def before_request():
     """Update requests per second stats."""
@@ -23,6 +35,8 @@ def before_request():
 def stop():
     import time
 
+    global pdb
+
     def get_inspect():
         from requests import get
         resp = get(current_app.url_for('tasks.get_info', _external=True))
@@ -63,7 +77,7 @@ def get_inspect():
     socketio.stop()
     print("Shutting down SocketIO web server!")
 
-    if pdb:
+    if 'pdb' in globals():
         del pdb
     print("Shutting down provdb!")
 

server/tasks.py

@@ -4,7 +4,7 @@
 except ImportError:  # pragma:  no cover
     from cStringIO import StringIO as BytesIO
 
-from flask import Blueprint, abort, current_app, g, request
+from flask import Blueprint, Flask, abort, current_app, g, request
 from werkzeug.exceptions import InternalServerError
 from celery import states
 

webserver/run_webserver.sh

@@ -44,7 +44,7 @@ else
 fi
 
 echo "create db ..."
-python3.8 manager.py createdb
+python3.8 manager.py createdb &
 
 echo "run redis ..."
 webserver/run-redis.sh &