run_3podR.sh

#!/bin/bash

# --- 1. CHECK FOR DOCKER INSTALLATION ---
if ! [ -x "$(command -v docker)" ]; then
    echo "🚀 Docker not found. Detecting OS for installation..."
    OS_TYPE="$(uname -s)"

    if [[ "$OS_TYPE" == "Darwin" ]]; then
        echo "🍎 Mac detected. Checking for Homebrew..."
        if ! [ -x "$(command -v brew)" ]; then
            echo "🍺 Homebrew not found. Installing Homebrew..."
            /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" <<EOF
EOF
            if [[ -f /opt/homebrew/bin/brew ]]; then
                eval "$(/opt/homebrew/bin/brew shellenv)"
            elif [[ -f /usr/local/bin/brew ]]; then
                eval "$(/usr/local/bin/brew shellenv)"
            fi
        fi
        echo "📦 Installing Docker Desktop via Homebrew..."
        brew install --cask docker
        open /Applications/Docker.app

    elif [[ "$OS_TYPE" == *"NT"* || "$OS_TYPE" == *"MINGW"* || "$OS_TYPE" == *"MSYS" ]]; then
        echo "🪟 Windows detected. Using winget..."
        if command -v winget.exe >/dev/null 2>&1; then
            echo "📦 Installing Docker Desktop via winget..."
            winget.exe install --id Docker.DockerDesktop --silent --accept-source-agreements --accept-package-agreements
            echo "🚀 Starting Docker Desktop..."
            "/c/Program Files/Docker/Docker Desktop.exe" & 
        else
            echo "❌ winget not found. Please install Docker manually: https://www.docker.com"
            exit 1
        fi
    else
        echo "❌ Unsupported OS."
        exit 1
    fi
fi

# --- 2. WAIT FOR DOCKER ENGINE ---
echo "🐋 Waiting for Docker engine to start..."
MAX_RETRIES=60 
COUNT=0
until docker info >/dev/null 2>&1; do
    echo "  ...still waiting (attempt $COUNT/60)..."
    sleep 10
    ((COUNT++))
    if [ $COUNT -ge $MAX_RETRIES ]; then
        echo "⏱️ Timeout: Docker engine didn't start. If this is a fresh install, a RESTART may be required."
        exit 1
    fi
done
echo "✅ Docker engine is ready!"

# --- 3. PREPARE LOCAL ENVIRONMENT ---
mkdir -p results
echo "📂 Host working directory: $(pwd)"
echo "📂 Host results folder contents before running container:"
ls -l results

# --- 4. PULL AND RUN ---
echo "📥 Pulling latest container..."
docker pull cdrl/3podr_container:latest

echo "📊 Running 3PodR Report..."

# --- 4a. Mount host files into container ---
docker run --rm \
  -v "$(pwd)/results":/project/results \
  -v "$(pwd)/extdata":/project/extdata \
  -v "$(pwd)/configuration.yml":/project/configuration.yml \
  -w /project \
  -e R_LIBS_USER=/opt/renv/library \
  -e R_PROFILE_USER=/dev/null \
  cdrl/3podr_container:latest \
  R -e '
    cat("📂 Inside container: current working directory:\n")
    print(getwd())
    cat("📄 Inside container: files in current directory before render:\n")
    print(list.files())
    dir.create("results", showWarnings = FALSE)
    cat("📄 Inside container: files in results/ after creation:\n")
    print(list.files("results"))
    bookdown::render_book(input = ".", output_dir = "results")
    cat("📄 Inside container: files in results/ after render_book:\n")
    print(list.files("results"))
    saveRDS(global_state, file = "results/global_state.rds")
  '

# --- 5. VERIFY ---
echo "📂 Host results folder contents after running container:"
ls -l results

if [ -n "$(ls -A results)" ]; then
    echo "✅ Done! Analysis successful. Files are in the 'results' folder."
else
    echo "❌ Error: Analysis finished but no files were found in 'results'."
    echo "Make sure your R Markdown outputs are correctly configured."
    exit 1
fi