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create workbench-jupyter-docker devcontainer to support docker workflows (#171)
* create workbench-jupyter-docker devcontainer to support docker workflows * lint * small comment
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‎src/workbench-jupyter-docker/.devcontainer.json

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{
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"name": "Workbench JupyterLab with docker support devcontainer template",
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"dockerComposeFile": "docker-compose.yaml",
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"service": "app",
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"shutdownAction": "none",
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"workspaceFolder": "/workspace",
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// Get the host's docker group ID and propagate it into the .env file, which
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// allows it to be used within docker-compose.yaml.
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"initializeCommand": "DOCKER_GID=`getent group docker | cut -d: -f3` && echo \"DOCKER_GID=${DOCKER_GID}\" > .env",
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"postCreateCommand": "./startupscript/post-startup.sh jupyter /home/jupyter ${templateOption:cloud} ${templateOption:login} && ./startupscript/setup-docker.sh",
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// re-mount bucket files on container start up
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"postStartCommand": [
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"./startupscript/remount-on-restart.sh",
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"jupyter",
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"/home/jupyter",
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"${templateOption:cloud}",
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"${templateOption:login}"
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],
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"remoteUser": "root",
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"customizations": {
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"workbench": {
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"opens": {
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"extensions": [
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// Source
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".ipynb",
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".R",
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".py",
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// Documents
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".md",
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".html",
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".latex",
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".pdf",
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// Images
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".bmp",
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".gif",
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".jpeg",
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".jpg",
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".png",
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".svg",
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// Data
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".csv",
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".tsv",
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".json",
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".vl"
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],
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"fileUrlSuffix": "/lab/tree/{path}",
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"folderUrlSuffix": "/lab/tree/{path}"
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}
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}
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}
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}

‎src/workbench-jupyter-docker/README.md

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# Custom Workbench JupyterLab App Template (workbench-jupyter-docker)
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A template used to serve the Workbench custom JupyterLab app.
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## Options
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| Options Id | Description | Type | Default Value |
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|-----|-----|-----|-----|
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| cloud | VM cloud environment | string | gcp |
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| login | Whether to log in to workbench CLI | string | false |
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---
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_Note: This file was auto-generated from the [devcontainer-template.json](devcontainer-template.json). Add additional notes to a `NOTES.md`._

‎src/workbench-jupyter-docker/devcontainer-template.json

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{
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"id": "custom-workbench-jupyter-template",
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"description": "A template used to serve the Workbench JupyterLab container image",
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"version": "0.0.1",
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"name": "Workbench Prebuilt JupyterLab Template",
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"documentationURL": "https://github.com/verily-src/workbench-app-devcontainers/tree/master/src/custom-workbench-jupyter-template",
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"licenseURL": "https://github.com/verily-src/workbench-app-devcontainers/blob/master/LICENSE",
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"options": {
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"cloud": {
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"type": "string",
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"description": "VM cloud environment",
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"proposals": ["gcp", "aws"],
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"default": "gcp"
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},
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"login": {
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"type": "string",
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"description": "Whether to log in to workbench CLI",
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"proposals": ["true", "false"],
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"default": "false"
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}
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},
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"platforms": ["Any"]
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}

‎src/workbench-jupyter-docker/docker-compose.yaml

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version: "2.4"
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services:
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app:
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container_name: "application-server"
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image: "us-central1-docker.pkg.dev/verily-workbench-public/apps/workbench-jupyter:latest"
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user: "jupyter:${DOCKER_GID}"
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restart: always
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volumes:
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- .:/workspace:cached
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# mount Host machine's docker.sock to container's docker.sock
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- /var/run/docker.sock:/var/run/docker.sock
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# mount Host machine's /etc/group to container's /etc/host-group
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- /etc/group:/etc/host-group
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# mount Host machine's default docker config dir to container's jupyter user docker config dir
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- /etc/docker:/home/jupyter/.docker
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ports:
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- "8888:8888"
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networks:
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- app-network
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cap_add:
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- SYS_ADMIN
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devices:
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- /dev/fuse
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security_opt:
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- apparmor:unconfined
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networks:
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app-network:
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external: true

‎startupscript/setup-docker.sh

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#!/bin/bash
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# setup-docker.sh
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# Installs the docker CLI and configure the host machine's docker group to
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# include the app container user.
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set -o errexit
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set -o nounset
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set -o pipefail
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set -o xtrace
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######################
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# Install Docker CLI #
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######################
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mkdir -p /etc/apt/keyrings && \
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curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /etc/apt/keyrings/docker.gpg && \
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echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null && \
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apt-get update && \
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apt-get install -y docker-ce-cli && \
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###########################################
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# Add container user to host docker group #
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###########################################
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# Add jupyter user to the host's docker group
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sed "/^docker:/ s/$/,jupyter/" /etc/host-group > /tmp/host-group.modified
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tee /etc/host-group < /tmp/host-group.modified > /dev/null
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# create a matching docker group in the container and add the user to it
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DOCKER_GID=$(grep '^docker:' "/etc/host-group" | cut -d: -f3)
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if ! getent group docker; then
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groupadd -g "$DOCKER_GID" docker
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fi
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usermod -aG docker jupyter
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###########################
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# Configuring docker auth #
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###########################
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# Give user write permissions to the mounted docker config directory
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chown -R jupyter /home/jupyter/.docker
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# Login to docker with gcloud credentials (needs to be re-run every 30 min if needed)
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sudo -u jupyter /bin/bash -c "docker login -u oauth2accesstoken -p $(gcloud auth print-access-token) https://us-central1-docker.pkg.dev"

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