a8c59b7cf0
Update documentation to reflect that all tools are provided via a builder Docker image - Simplify prerequisites section in Readme.md - Add detailed explanation of the builder image and its role - Document R package caching mechanism for faster builds - Update start-jupyterhub.sh to build and use the builder image - Add Dockerfile.builder to provide the build environment - Implement automatic R dependency detection and installation - Update Slides.qmd to use gt package for better table formatting
304 lines
9.0 KiB
Bash
Executable File
304 lines
9.0 KiB
Bash
Executable File
#!/bin/bash
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# JupyterHub startup script for labs
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# Usage: ./start-jupyterhub.sh [--no-build|--offline] [--force-rebuild] [--stop-server] [--update-lectures] [--build-obidoc]
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set -e
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SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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DOCKER_DIR="${SCRIPT_DIR}/obijupyterhub/"
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BUILDER_IMAGE="obijupyterhub-builder:latest"
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# Colors for display
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GREEN='\033[0;32m'
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BLUE='\033[0;34m'
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YELLOW='\033[1;33m'
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NC='\033[0m' # No Color
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NO_BUILD=false
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FORCE_REBUILD=false
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STOP_SERVER=false
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UPDATE_LECTURES=false
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BUILD_OBIDOC=false
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usage() {
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cat <<EOF
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Usage: ./start-jupyterhub.sh [options]
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Options:
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--no-build | --offline Skip Docker image builds (use existing images)
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--force-rebuild Rebuild images without cache
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--stop-server Stop the stack and remove student containers, then exit
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--update-lectures Rebuild the course website only (no Docker stop/start)
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--build-obidoc Force rebuild of obidoc documentation
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-h, --help Show this help
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EOF
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}
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while [[ $# -gt 0 ]]; do
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case "$1" in
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--no-build|--offline) NO_BUILD=true ;;
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--force-rebuild) FORCE_REBUILD=true ;;
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--stop-server) STOP_SERVER=true ;;
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--update-lectures) UPDATE_LECTURES=true ;;
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--build-obidoc) BUILD_OBIDOC=true ;;
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-h|--help) usage; exit 0 ;;
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*) echo "Unknown option: $1" >&2; usage; exit 1 ;;
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esac
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shift
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done
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if $STOP_SERVER && $UPDATE_LECTURES; then
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echo "Error: --stop-server and --update-lectures cannot be used together" >&2
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exit 1
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fi
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echo "Starting JupyterHub for Lab"
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echo "=============================="
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echo ""
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echo -e "${BLUE}Building the volume directories...${NC}"
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pushd "${SCRIPT_DIR}/jupyterhub_volumes" >/dev/null
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mkdir -p caddy/data
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mkdir -p caddy/config
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mkdir -p course/bin
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mkdir -p course/R_packages
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mkdir -p jupyterhub
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mkdir -p shared
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mkdir -p users
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mkdir -p web/obidoc
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mkdir -p builder/R_packages
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popd >/dev/null
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pushd "${DOCKER_DIR}" >/dev/null
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# Check we're in the right directory
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if [ ! -f "Dockerfile" ] || [ ! -f "docker-compose.yml" ]; then
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echo "Error: Run this script from the jupyterhub-tp/ directory"
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exit 1
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fi
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check_if_image_needs_rebuild() {
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local image_name="$1"
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local dockerfile="$2"
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# Check if image exists
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if ! docker image inspect "$image_name" >/dev/null 2>&1; then
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return 0 # Need to build (image doesn't exist)
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fi
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# If force rebuild, always rebuild
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if $FORCE_REBUILD; then
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return 0 # Need to rebuild
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fi
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# Compare Dockerfile modification time with image creation time
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if [ -f "$dockerfile" ]; then
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local dockerfile_mtime=$(stat -c %Y "$dockerfile" 2>/dev/null || echo 0)
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local image_created=$(docker image inspect "$image_name" --format='{{.Created}}' 2>/dev/null | sed 's/\.000000000//' | xargs -I {} date -d "{}" +%s 2>/dev/null || echo 0)
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if [ "$dockerfile_mtime" -gt "$image_created" ]; then
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echo -e "${YELLOW}Dockerfile is newer than image, rebuild needed${NC}"
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return 0 # Need to rebuild
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fi
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fi
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return 1 # No need to rebuild
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}
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build_builder_image() {
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if check_if_image_needs_rebuild "$BUILDER_IMAGE" "Dockerfile.builder"; then
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local build_flag=()
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if $FORCE_REBUILD; then
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build_flag+=(--no-cache)
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fi
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echo ""
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echo -e "${BLUE}Building builder image...${NC}"
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docker build "${build_flag[@]}" -t "$BUILDER_IMAGE" -f Dockerfile.builder .
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else
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echo -e "${BLUE}Builder image is up to date, skipping build.${NC}"
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fi
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}
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# Run a command inside the builder container with the workspace mounted
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# R packages are persisted in jupyterhub_volumes/builder/R_packages
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# R_LIBS includes both the builder packages (attachment) and the mounted volume
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run_in_builder() {
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docker run --rm \
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-v "${SCRIPT_DIR}:/workspace" \
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-v "${SCRIPT_DIR}/jupyterhub_volumes/builder/R_packages:/usr/local/lib/R/site-library" \
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-e "R_LIBS=/opt/R/builder-packages:/usr/local/lib/R/site-library" \
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-w /workspace \
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"$BUILDER_IMAGE" \
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bash -c "$1"
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}
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stop_stack() {
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echo -e "${BLUE}Stopping existing containers...${NC}"
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docker-compose down 2>/dev/null || true
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echo -e "${BLUE}Cleaning up student containers...${NC}"
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docker ps -aq --filter name=jupyter- | xargs -r docker rm -f 2>/dev/null || true
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}
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build_images() {
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if $NO_BUILD; then
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echo -e "${YELLOW}Skipping image builds (offline/no-build mode).${NC}"
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return
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fi
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local build_flag=()
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if $FORCE_REBUILD; then
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build_flag+=(--no-cache)
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fi
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# Check and build student image
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if check_if_image_needs_rebuild "jupyterhub-student:latest" "Dockerfile"; then
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echo ""
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echo -e "${BLUE}Building student image...${NC}"
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docker build "${build_flag[@]}" -t jupyterhub-student:latest -f Dockerfile .
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else
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echo -e "${BLUE}Student image is up to date, skipping build.${NC}"
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fi
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# Check and build JupyterHub image
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if check_if_image_needs_rebuild "jupyterhub-hub:latest" "Dockerfile.hub"; then
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echo ""
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echo -e "${BLUE}Building JupyterHub image...${NC}"
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docker build "${build_flag[@]}" -t jupyterhub-hub:latest -f Dockerfile.hub .
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else
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echo -e "${BLUE}JupyterHub image is up to date, skipping build.${NC}"
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fi
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}
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build_obidoc() {
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local dest="${SCRIPT_DIR}/jupyterhub_volumes/web/obidoc"
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if $NO_BUILD; then
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echo -e "${YELLOW}Skipping obidoc build in offline/no-build mode.${NC}"
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return
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fi
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local needs_build=false
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if $BUILD_OBIDOC; then
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needs_build=true
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elif [ -z "$(ls -A "$dest" 2>/dev/null)" ]; then
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needs_build=true
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fi
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if ! $needs_build; then
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echo -e "${BLUE}obidoc already present; skipping rebuild (use --build-obidoc to force).${NC}"
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return
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fi
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echo ""
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echo -e "${BLUE}Building obidoc documentation (in builder container)...${NC}"
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run_in_builder '
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set -e
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BUILD_DIR=$(mktemp -d)
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cd "$BUILD_DIR"
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git clone --recurse-submodules \
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--remote-submodules \
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-j 8 \
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https://github.com/metabarcoding/obitools4-doc.git
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cd obitools4-doc
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hugo -D build --baseURL "/obidoc/"
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mkdir -p /workspace/jupyterhub_volumes/web/obidoc
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rm -rf /workspace/jupyterhub_volumes/web/obidoc/*
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mv public/* /workspace/jupyterhub_volumes/web/obidoc/
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cd /
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rm -rf "$BUILD_DIR"
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'
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}
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build_website() {
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echo ""
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echo -e "${BLUE}Building web site (in builder container)...${NC}"
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run_in_builder '
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set -e
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echo "-> Detecting and installing R dependencies..."
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Rscript /workspace/tools/install_quarto_deps.R /workspace/web_src
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echo "-> Rendering Quarto site..."
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cd /workspace/web_src
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quarto render
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find . -name "*.pdf" -print | while read pdfname; do
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dest="/workspace/jupyterhub_volumes/web/pages/${pdfname}"
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dirdest=$(dirname "$dest")
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mkdir -p "$dirdest"
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cp "$pdfname" "$dest"
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done
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python3 /workspace/tools/generate_pdf_galleries.py
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python3 /workspace/tools/generate_pages_json.py
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'
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}
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start_stack() {
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echo ""
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echo -e "${BLUE}Starting JupyterHub...${NC}"
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docker-compose up -d --remove-orphans
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echo ""
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echo -e "${YELLOW}Waiting for JupyterHub to start...${NC}"
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sleep 3
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}
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print_success() {
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if docker ps | grep -q jupyterhub; then
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echo ""
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echo -e "${GREEN}JupyterHub is running!${NC}"
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echo ""
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echo "-------------------------------------------"
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echo -e "${GREEN}JupyterHub available at: http://localhost:8888${NC}"
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echo "-------------------------------------------"
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echo ""
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echo "Password: metabar2025"
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echo "Students can connect with any username"
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echo ""
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echo "Admin account:"
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echo " Username: admin"
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echo " Password: admin2025"
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echo ""
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echo "Each student will have access to:"
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echo " - work/ : personal workspace (everything saved)"
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echo " - work/R_packages/ : personal R packages (writable)"
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echo " - work/shared/ : shared workspace"
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echo " - work/course/ : course files (read-only)"
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echo " - work/course/R_packages/ : shared R packages by prof (read-only)"
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echo " - work/course/bin/ : shared executables (in PATH)"
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echo ""
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echo "To view logs: docker-compose logs -f jupyterhub"
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echo "To stop: docker-compose down"
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echo ""
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else
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echo ""
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echo -e "${YELLOW}JupyterHub container doesn't seem to be starting${NC}"
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echo "Check logs with: docker-compose logs jupyterhub"
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exit 1
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fi
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}
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if $STOP_SERVER; then
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stop_stack
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popd >/dev/null
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exit 0
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fi
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if $UPDATE_LECTURES; then
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build_builder_image
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build_website
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popd >/dev/null
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exit 0
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fi
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stop_stack
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build_builder_image
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build_images
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build_website
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build_obidoc
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start_stack
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popd >/dev/null
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print_success
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