SORMAS-Stats-next-gen

SORMAS-Stats contain functions to analyze and visualize surveillance data collected by SORMAS.

Run docker container

Prerequisites

(1) You should begin this tutorial after installing and configuring the SORMAS app on your system, and create some data in the database. Information on how to install SORMAS can be found on the SORMAS-Docker repository https://github.com/hzi-braunschweig/SORMAS-Docker.

(2) You need to install a container engine (e.g. Docker)

Run container

(3) Pull the latests version from hub.docker.com

docker pull hzibraunschweig/sormas-stats:latest

If you like to pull an image built from development branch, you need to pull the tag 'developemnt'.

(4) Run the image

docker run -p 0.0.0.0:3838:3838 hzibraunschweig/sormas-stats:latest

The app will listen on port 3838. You can map this port to any port on the server.

docker run -p 0.0.0.0:3838:3838 -v /local_path_to_app/shiny-server.conf:/etc/shiny-server/shiny-server.conf hzibraunschweig/sormas-stats:latest

If you like to provide a custom shiny-server.conf you can map this as a volume. For example shiny-server.conf:

 # Instruct Shiny Server to run applications as the user "shiny"
run_as shiny;

# Define a server that listens on port 3838
server {
  listen 3838 0.0.0.0;

  # Define a location at the base URL
  location / {

    # Host the directory of Shiny Apps stored in this directory
    site_dir /srv/shiny-server;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

    # When a user visits the base URL rather than a particular application,
    # an index of the applications available in this directory will be shown.
    directory_index on;
  }
}

Please refer to the documentation of R shiny https://docs.rstudio.com/shiny-server/#default-configuration

Environment parameters

After starting the container, the application tries to connect to a SORMAS database. The container uses these environment parameters for configuration:

Parameter	default	accepted values
SHINY_LOG_STDERR		0 or 1 to log output of the app to stderr (needed to display via docker-logs)
DB_USER	"sormas_user"	username for sormas databse
DB_PASS	"password"	password of database user
DB_HOST	127.0.0.1	IP-Adress of SORMAS database to connect to
DB_PORT	5432	SORMAS database port
DB_NAME	"sormas"	name of sormas database

Docker compose

You can use a docker-compose file to start the application:

version: "3"
services: 
  sormas-stats:
    ports: 
      - "0.0.0.0:3838:3838"
    image: hzibraunschweig/sormas-stats:latest      
    environment: 
      - SHINY_LOG_STDERR=1
      - DB_USER="sormas_user"
      - DB_PASS="{{ sormas.postgres.password }}"
      - DB_HOST="{{ ansible_default_ipv4.address }}"
      - DB_PORT="5432"
      - DB_NAME="sormas"
    volumes: 
      - /path_to_shiny_app/shiny-server.conf:/etc/shiny-server/shiny-server.conf
    restart: always

Run locally

(1) Set the R PATH to where the example-app.Rproj is saved on your sytem. You can also double click on example-app.Rproj to launch R and this would automatically set the PATH.

setwd("SORMAS-Stats/shinyapp")

(2) Run app using the command shiny::runApp()

hzi-braunschweig / SORMAS-Stats-next-gen

readme