To deploy the apps using Ansible you need the key pair that you use to connect to the EC2 instance, likely this file is called WATER.pem
Cloned this repository to your local machine, run this command:
git clone https://github.com/WSWCWaterDataExchange/Apps
Now that you have the key pair and the cloned project, open a terminal on your local machine and change directory to the ansible folder of the cloned repository. You may want to check the Ansible documentation on the README.md file on this folder, to learn about the parameters you can change to customize the deployment: https://github.com/WSWCWaterDataExchange/Apps/tree/master/ansible#ansible-playbooks
When you are done customizing, run this command to deploy:
ansible-playbook -i hosts deploy.yml --private-key /<path-to-the-ec2-key>/WATER.pem
e. g:
ansible-playbook -i hosts deploy.yml --private-key /home/user/my-aws-keys/WATER.pem
If you want to add more shiny applications on this repository you just need to copy the application folder into the root of this repository and follow the instructions here https://github.com/WSWCWaterDataExchange/Apps/tree/master/ansible#shiny_serverj2
to add its configuration for the nginx webserver. There is an scenario when adding a new shiny application brings new dependencies to the mix, in this case it is necesary to figure out what is the dependency missing and once found, add it to the dockerfile.j2 template. This process of finding missing dependencies may need a development environment so it won't be covered in full detail in this document.
From time to time you may need to update the source code of your shiny applications. It's very important that you check if the new code uses software that was not previously on the docker image dependencies dockerfile.j2.
Inside the shiny applications folder is likely to see a file named global.R where the dependencies names are stated, if not then at the beginning of the server.R file. What you need to do is to make sure that all the library names required by your applications are also on the dockerfile.j2 file.
e. g:
Suppose your shiny application has the following list of required libraries on it's code:
library(ggplot2)
library(XML)
library(RColorBrewer)
library(RCurl)
library(plotly)
then you must make sure that your dockerfile.j2 looks like this:
FROM rocker/shiny:latest
RUN apt update && apt install -y libxml2-dev libssl-dev
RUN install.r ggplot2 XML RCurl plotrix plotly
EXPOSE 3838
WORKDIR /srv/shiny-server
it's not an obvious fact to notice, but the libray plotly also requires a system dependency to be installed, that's why libssl-dev is listed on the system packages dependencies list. So the recommendation is to make a little research about the new dependencies to make sure you add all the kind of dependencies you need.
If you update the shiny apps source, then deploy and the result is that the apps are no longer working, here are some things you can try. First login into the container with the command docker exec -it shiny bash then run cat /var/log/shiny-server/*. You will see a lot of output which will hopefully provide insights about packages that were not correctly installed, most likely because of unmet dependencies.
Then you can try to install those packages manually with the following command
# if it's a system library
# system library name's are not always easy to figure out
# so you may need to research a bit on google
apt install <library-name>
# if it's an R package
install.r <package-name>
# if it's a github package
installGithub.r <github-user/repository-name>
After trying manual installation and checking that dependencies are met, exit the container with ctrl + d and then try restarting the shiny and nginx containers
docker restart shiny
docker restart nginx
If you want to uninstall the shiny applications run the following commands from the EC2 instance, to remove the nginx virtualhost
# It is assumed that the 'clone_location' variable is set to "/home/ubuntu/env"
# if not, you need to change the code below to reflect its actual value
sudo rm -f /home/ubuntu/env/conf.d/shiny.conf
and then to remove the container
# Same as above, if you changed the 'shiny_container' variable value then you have
# to reflect the changes in the code below
sudo docker rm -f shiny
lastly restart the nginx container
sudo docker restart nginx