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setup_notes.md

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Server & Scheduling Setup Notes

These notes are for configuring the Shiny Server deployment, scheduled updates, and system-level setup on our VM.

Shiny Server Setup

See lab documentation for full instructions. (Access required)

Key location on the server

/srv/shiny-server/shiny-performance-tracking

System-wide R Package Installation

To install R packages for all users on akramihpc1, switch to superuser:

sudo -i
R
# Then install packages as root
install.packages("shiny")

Scheduled Data Processing

Data updates and Git syncs are handled automatically via a daily cron job + systemd timer.

Crontab Script: /etc/cron.daily/update_shiny_app.sh

#!/bin/bash

# Fail on error, unset variable, or pipe failure
set -euo pipefail

# For cron jobs, explicitly set $HOME
export HOME=/root/

# Timestamp for log file name
DATE=$(date +"%Y-%m-%d_%H-%M")
LOG_FILE="/mnt/ceph/_logs/shiny_log_$DATE.txt"

# Function for logging
log() {
    echo "[$(date '+%Y-%m-%d %H:%M:%S')] $1" | tee -a "$LOG_FILE"
}

# Function for error handling
handle_error() {
    log "ERROR: An error occurred in the script at line $1"
    log "Last command exit code: $2"
    exit 1
}

# Set up error handling
trap 'handle_error ${LINENO} $?' ERR

# Start logging
log "===== SCRIPT START ====="

# Check if required directories exist
if [ ! -d "/srv/shiny-server/shiny-performance-tracking" ]; then
    log "ERROR: Application directory not found"
    exit 1
fi

if [ ! -d "/mnt/ceph/_logs" ]; then
    log "ERROR: Log directory not found"
    exit 1
fi

# Change to application directory
cd /srv/shiny-server/shiny-performance-tracking || {
    log "ERROR: Failed to change to application directory"
    exit 1
}

# Ensure git is configured for this directory
git config --global --add safe.directory /srv/shiny-server/shiny-performance-tracking

# Git operations with error checking
log "Checking out master branch..."
if ! git checkout master; then
    log "ERROR: Failed to checkout master branch"
    exit 1
fi

log "Pulling latest changes..."
if ! git pull; then
    log "ERROR: Failed to pull latest changes"
    exit 1
fi

# Run R script with error checking
log "Running R script..."
if ! Rscript ExtractSaveData.R; then
    log "ERROR: R script failed"
    exit 1
fi

# Check for changes and handle git operations
log "Checking for changes..."
if ! git diff --quiet; then
    log "Changes detected. Committing and pushing..."
    if ! git add .; then
        log "ERROR: Failed to add changes"
        exit 1
    fi

    if ! git commit -m "daily update of TRAINING.csv"; then
        log "ERROR: Failed to commit changes"
        exit 1
    fi

    if ! git push; then
        log "ERROR: Failed to push changes"
        exit 1
    fi

    log "Restarting shiny-server..."
    if ! systemctl restart shiny-server.service; then
        log "ERROR: Failed to restart shiny-server"
        exit 1
    fi
else
    log "No changes to commit. Skipping push and restart."
fi

log "===== SCRIPT END ====="

# Exit successfully
exit 0

Systemd Configuration

  • /etc/systemd/system/update_shiny_app.service
  • /etc/systemd/system/update_shiny_app.timer

Use systemctl to manage:

sudo systemctl daemon-reload      # Reload config after edits
systemctl list-timers             # View active timers

SSH Key for Git Push (as root)

The cron job runs as root, so it needs a GitHub SSH key added for the root user.

See: GitHub’s SSH setup guide

Related Lab Docs