Update Jupyter UI (#225)

* Updating notebooks (autorun + skiping init cell) * adding /lab support for jupyter * updating jupyter version * enabling init_cell by default * updating bootstrap script * PR comments
DataDog · Jul 18, 2024 · 265f490 · 265f490
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diff --git a/deployments/kubehound/docker-compose.yaml b/deployments/kubehound/docker-compose.yaml
@@ -37,6 +37,7 @@ services:
       - jupyter
     ports:
       - "127.0.0.1:8888:8888"
+      - "127.0.0.1:8889:8889"
     networks:
       - kubenet
     labels:
@@ -45,6 +46,7 @@ services:
       - kubeui_data:/root/notebooks/shared
     environment:
       - NOTEBOOK_PASSWORD=admin
+      - GRAPH_NOTEBOOK_SSL=False
 
   ui-invana-engine:
     image: invanalabs/invana-engine:latest

diff --git a/deployments/kubehound/notebook/BlueTeam.ipynb b/deployments/kubehound/notebook/BlueTeam.ipynb
@@ -15,40 +15,17 @@
    "source": [
     "## Initial Setup\n",
     "\n",
-    "Connect to the kubegraph server by running the cell below"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%graph_notebook_config\n",
-    "{\n",
-    "  \"host\": \"kubegraph\",\n",
-    "  \"port\": 8182,\n",
-    "  \"ssl\": false,\n",
-    "  \"gremlin\": {\n",
-    "    \"traversal_source\": \"g\",\n",
-    "    \"username\": \"\",\n",
-    "    \"password\": \"\",\n",
-    "    \"message_serializer\": \"graphsonv3\"\n",
-    "  }\n",
-    "}"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
+    "Connection is being initated directly from the docker using the env vars `GRAPH_NOTEBOOK_HOST` and `GRAPH_NOTEBOOK_PORT`. To overwrite it you can use the magic `%%graph_notebook_config` [details here](https://github.com/aws/graph-notebook/tree/main/additional-databases/gremlin-server#connecting-to-a-local-gremlin-server-from-jupyter).\n",
+    "\n",
     "Now set the appearance customizations for the notebook. You can see a guide on possible options [here](https://github.com/aws/graph-notebook/blob/623d43827f798c33125219e8f45ad1b6e5b29513/src/graph_notebook/notebooks/01-Neptune-Database/02-Visualization/Grouping-and-Appearance-Customization-Gremlin.ipynb#L680)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "init_cell": true
+   },
    "outputs": [],
    "source": [
     "%%graph_notebook_vis_options\n",

diff --git a/deployments/kubehound/notebook/Dockerfile b/deployments/kubehound/notebook/Dockerfile
@@ -1,75 +1,109 @@
 # This Dockerfile is a tailored version of https://github.com/aws/graph-notebook under APACHE 2 LICENCE
 
-FROM amazonlinux:2
+FROM amazonlinux:2022
 
 # Notebook Port
 EXPOSE 8888
 # Lab Port
 EXPOSE 8889
-USER root
 
+# May need to be set to `pipargs=' -i https://pypi.tuna.tsinghua.edu.cn/simple '` for china regions
 ENV pipargs=""
-ENV WORKING_DIR="/root"
+ENV WORKING_DIR="/kubehound"
 ENV NOTEBOOK_DIR="${WORKING_DIR}/notebooks"
-ENV NODE_VERSION=14.x
+ENV EXAMPLE_NOTEBOOK_DIR="${NOTEBOOK_DIR}/kubehound_presets"
+ENV NODE_VERSION=14
+ENV PYTHON_VERSION=3.10
 ENV GRAPH_NOTEBOOK_AUTH_MODE="DEFAULT"
 ENV GRAPH_NOTEBOOK_HOST="kubegraph"
+ENV GRAPH_NOTEBOOK_PROXY_PORT="8192"
+ENV GRAPH_NOTEBOOK_PROXY_HOST=""
 ENV GRAPH_NOTEBOOK_PORT="8182"
+ENV NEPTUNE_LOAD_FROM_S3_ROLE_ARN=""
+ENV AWS_REGION="us-east-1"
 ENV NOTEBOOK_PORT="8888"
 ENV LAB_PORT="8889"
 ENV GRAPH_NOTEBOOK_SSL="True"
+ENV NOTEBOOK_PASSWORD="admin"
+ENV PROVIDE_EXAMPLES=0
 
 # "when the SIGTERM signal is sent to the docker process, it immediately quits and all established connections are closed"
 # "graceful stop is triggered when the SIGUSR1 signal is sent to the docker process"
 STOPSIGNAL SIGUSR1
 
+ENV GID 1000
+ENV UID 1000
+
+# Update the package list, install sudo, create a non-root user, and grant password-less sudo permissions
+RUN yum update -y && \
+    yum install -y sudo shadow-utils && \
+    /usr/sbin/groupadd --gid $GID nonroot && \
+    adduser --uid $UID --gid $GID --system nonroot -m && \
+    echo 'nonroot ALL=(ALL) NOPASSWD: ALL' >> /etc/sudoers
 
 RUN mkdir -p "${WORKING_DIR}" && \
     mkdir -p "${NOTEBOOK_DIR}" && \
+    mkdir -p "${EXAMPLE_NOTEBOOK_DIR}" && \
+    chown -R nonroot:nonroot "${WORKING_DIR}" && \
     # Yum Update and install dependencies
     yum update -y && \
-    yum install tar gzip git amazon-linux-extras which -y && \
+    yum install tar gzip git findutils -y && \
     # Install NPM/Node
-    curl --silent --location https://rpm.nodesource.com/setup_${NODE_VERSION} | bash - && \
-    yum install nodejs -y && \
-    npm install -g opencollective && \
-    # Install Python 3.8
-    amazon-linux-extras install python3.8 -y && \
-    update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1 && \
+    curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.3/install.sh | bash && \
+    . ~/.nvm/nvm.sh && \
+    nvm install ${NODE_VERSION} && \
+    # Install Python
+    yum install python${PYTHON_VERSION} -y && \
+    # update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 1 && \
     echo 'Using python version:' && \
-    python3 --version && \
-    python3 -m ensurepip --upgrade  && \
-    python3 -m venv /tmp/venv && \
+    python${PYTHON_VERSION} --version && \
+    python${PYTHON_VERSION} -m ensurepip --upgrade  && \
+    python${PYTHON_VERSION} -m venv /tmp/venv && \
     source /tmp/venv/bin/activate && \
     cd "${WORKING_DIR}" && \
     # Clone the repo and install python dependencies
     git clone https://github.com/aws/graph-notebook && \
     cd "${WORKING_DIR}/graph-notebook" && \
+    chown -R nonroot:nonroot "${WORKING_DIR}/graph-notebook" && \
     pip3 install --upgrade pip setuptools wheel && \
     pip3 install twine==3.7.1 && \
     pip3 install -r requirements.txt && \
+    pip3 install --upgrade 'jupyter-server<2.0.0' && \
     pip3 install "jupyterlab>=3,<4" && \
+    pip3 install jupyter_contrib_nbextensions && \
+    pip3 install jupyter_nbextensions_configurator && \
     # Build the package
     python3 setup.py sdist bdist_wheel && \
     # install the copied repo
     pip3 install . && \
     # copy premade starter notebooks
     cd "${WORKING_DIR}/graph-notebook" && \
+    jupyter contrib nbextension install --system --debug && \
     jupyter nbextension enable  --py --sys-prefix graph_notebook.widgets && \
+    jupyter nbextensions_configurator enable --system  # can be skipped for notebook >=5.3 && \
     # This allows for the `.ipython` to be set
     python -m graph_notebook.start_jupyterlab --jupyter-dir "${NOTEBOOK_DIR}" && \
+    deactivate && \
     # Cleanup
     yum clean all && \
     yum remove wget tar git  -y && \
     rm -rf /var/cache/yum && \
     rm -rf "${WORKING_DIR}/graph-notebook" && \
     rm -rf /root/.cache && \
     rm -rf /root/.npm/_cacache && \
-    rm -rf /usr/share
+    cd /usr/share && \
+    rm -r $(ls -A | grep -v terminfo)
+
+# Set the non-root user as the default user
+USER nonroot
+
+ADD --chown=nonroot:nonroot *.ipynb ${EXAMPLE_NOTEBOOK_DIR}/
 
-ADD *.ipynb ${NOTEBOOK_DIR}/
+# Adding support for init_cell - allow cell to be run on startup of the notebook
+# Command not working jupyter nbextension enable --system init_cell && \
+ADD --chown=nonroot:nonroot notebook.json /home/nonroot/.jupyter/nbconfig/notebook.json
 
-ADD ./service.sh /usr/bin/service.sh
+ADD --chown=nonroot:nonroot ./service.sh /usr/bin/service.sh
 RUN chmod +x /usr/bin/service.sh
 
 ENTRYPOINT [ "bash","-c","service.sh" ]
diff --git a/deployments/kubehound/notebook/KindCluster_Demo.ipynb b/deployments/kubehound/notebook/KindCluster_Demo.ipynb
@@ -18,40 +18,17 @@
    "source": [
     "## Initial Setup\n",
     "\n",
-    "Connect to the kubegraph server by running the cell below"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%graph_notebook_config\n",
-    "{\n",
-    "  \"host\": \"kubegraph\",\n",
-    "  \"port\": 8182,\n",
-    "  \"ssl\": false,\n",
-    "  \"gremlin\": {\n",
-    "    \"traversal_source\": \"g\",\n",
-    "    \"username\": \"\",\n",
-    "    \"password\": \"\",\n",
-    "    \"message_serializer\": \"graphsonv3\"\n",
-    "  }\n",
-    "}"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
+    "Connection is being initated directly from the docker using the env vars `GRAPH_NOTEBOOK_HOST` and `GRAPH_NOTEBOOK_PORT`. To overwrite it you can use the magic `%%graph_notebook_config` [details here](https://github.com/aws/graph-notebook/tree/main/additional-databases/gremlin-server#connecting-to-a-local-gremlin-server-from-jupyter).\n",
+    "\n",
     "Now set the appearance customizations for the notebook. You can see a guide on possible options [here](https://github.com/aws/graph-notebook/blob/623d43827f798c33125219e8f45ad1b6e5b29513/src/graph_notebook/notebooks/01-Neptune-Database/02-Visualization/Grouping-and-Appearance-Customization-Gremlin.ipynb#L680)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "init_cell": true
+   },
    "outputs": [],
    "source": [
     "%%graph_notebook_vis_options\n",

diff --git a/deployments/kubehound/notebook/KubeHound.ipynb b/deployments/kubehound/notebook/KubeHound.ipynb
@@ -18,40 +18,17 @@
    "source": [
     "## Initial Setup\n",
     "\n",
-    "Connect to the kubegraph server by running the cell below"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "%%graph_notebook_config\n",
-    "{\n",
-    "  \"host\": \"kubegraph\",\n",
-    "  \"port\": 8182,\n",
-    "  \"ssl\": false,\n",
-    "  \"gremlin\": {\n",
-    "    \"traversal_source\": \"g\",\n",
-    "    \"username\": \"\",\n",
-    "    \"password\": \"\",\n",
-    "    \"message_serializer\": \"graphsonv3\"\n",
-    "  }\n",
-    "}"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
+    "Connection is being initated directly from the docker using the env vars `GRAPH_NOTEBOOK_HOST` and `GRAPH_NOTEBOOK_PORT`. To overwrite it you can use the magic `%%graph_notebook_config` [details here](https://github.com/aws/graph-notebook/tree/main/additional-databases/gremlin-server#connecting-to-a-local-gremlin-server-from-jupyter).\n",
+    "\n",
     "Now set the appearance customizations for the notebook. You can see a guide on possible options [here](https://github.com/aws/graph-notebook/blob/623d43827f798c33125219e8f45ad1b6e5b29513/src/graph_notebook/notebooks/01-Neptune-Database/02-Visualization/Grouping-and-Appearance-Customization-Gremlin.ipynb#L680)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "init_cell": true
+   },
    "outputs": [],
    "source": [
     "%%graph_notebook_vis_options\n",