├── .gitignore
├── README.md
├── application.yml
├── docker-compose.yml
├── nginx.conf
├── run_first_time.sh
└── webapp
    ├── Dockerfile
    ├── Rprofile.site
    ├── shinyapps
        └── app.R
    └── shinylog
        └── placeholder.txt


/.gitignore:
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1 | nginx/certs/localhost
2 | 


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/README.md:
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 1 | Telethon Kids Institute ShinyProxy Docker Template
 2 | ================
 3 | 
 4 | ### Docker Ubuntu Server Installation/Set-up
 5 | 
 6 | 1.  Docker CE for Ubuntu installation:
 7 |     <https://docs.docker.com/install/linux/docker-ce/ubuntu/>
 8 | 2.  Follow post-installation instructions:
 9 |     <https://docs.docker.com/install/linux/linux-postinstall/>
10 |     1.  configuring the daemon.json file will not work with Ubuntu 16.04
11 |         (and above), instead add the following to the systemd unit file:
12 |         `ExecStart=/usr/bin/dockerd -H fd:// -H tcp://127.0.0.1:275 -H
13 |         unix:///var/run/docker.sock`
14 | 3.  Install docker-compose <https://docs.docker.com/compose/install/>
15 |     (optional):
16 | 
17 | <!-- end list -->
18 | 
19 |     sudo curl -L "https://github.com/docker/compose/releases/download/1.24.0-rc1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
20 |     sudo chmod +x /usr/local/bin/docker-compose
21 |     sudo ln -s /usr/local/bin/docker-compose /usr/bin/docker-compose
22 | 
23 | ### Docker App Deployment
24 | 
25 | 1.  Build Shiny App Docker image:
26 |     1.  Change current directory to project folder `cd ...`
27 |     2.  `docker build -t telethonkids/new_shiny_app ./<project
28 |         directory>/webapp`
29 | 2.  Start Docker containers
30 |     3.  `docker-compose up -d`
31 | 3.  App is ready on port 80: in browser, go to 192.168.99.100 (windows)
32 |     or 127.17.0.1 (Ubuntu)
33 | 
34 | ### HTTPS encryption
35 | 
36 | [These instructions](https://medium.com/@pentacent/nginx-and-lets-encrypt-with-docker-in-less-than-5-minutes-b4b8a60d3a71)
37 | were used to set up a secure HTTPS connection with Certbot SSL certificates.
38 | Also see [here](https://github.com/wmnnd/nginx-certbot).
39 | 
40 | This will not work out of the box, the NGINX configuration file will need to be
41 | updated with your domain name (which is required) at the indicated places in
42 | `nginx.conf`. `init-letsencrypt.sh` also needs to be configured with your domain
43 | names(s) and email address.
44 | 
45 | The following commands will need to be run on the host machine in order to obtain
46 | the first valid certificates: first run `chmod +x init-letsencrypt.sh` then
47 | `./init-letsencrypt.sh`.
48 | 
49 | If HTTPS security is not wanted then you will need to remove the indicated chunks
50 | of code in `nginx.conf`.
51 | 


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/application.yml:
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 1 | proxy:
 2 |   title: Telethon Kids Institute Shiny Apps
 3 |   hide-navbar: false
 4 |   landing-page: /
 5 |   heartbeat-rate: 10000
 6 |   heartbeat-timeout: 600000
 7 |   port: 8080
 8 |   docker:
 9 |     internal-networking: true
10 |   specs:
11 |   - id: shiny_app
12 |     display-name: New Shiny App
13 |     description: The default app when initiating a new shiny app via. RStudio
14 |     container-cmd: ["R", "-e", "shiny::runApp('/root/app')"]
15 |     container-image: telethonkids/new_shiny_app
16 |     container-network: tki-net
17 |     container-env:
18 |       user: "shiny"
19 |       environment:
20 |         - APPLICATION_LOGS_TO_STDOUT=false
21 |   usage-stats-url: http://influxdb:8086/write?db=shinyproxy_usage
22 | 
23 | server:
24 |   useForwardHeaders: true
25 | 
26 | 


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/docker-compose.yml:
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 1 | version: "3.6"
 2 | services:
 3 |   nginx:
 4 |     image: nginx:alpine
 5 |     container_name: tki_nginx
 6 |     restart: on-failure
 7 |     networks:
 8 |       - tki-net
 9 |     volumes:
10 |       - ./nginx.conf:/etc/nginx/nginx.conf
11 |       - ./data/certbot/conf:/etc/letsencrypt
12 |       - ./data/certbot/www:/var/www/certbot
13 |     ports:
14 |       - 80:80
15 |       - 443:443
16 |     command: "/bin/sh -c 'while :; do sleep 6h & wait $${!}; nginx -s reload; done & nginx -g \"daemon off;\"'"
17 |     depends_on:
18 |       - shinyproxy
19 | 
20 |   certbot:
21 |     image: certbot/certbot
22 |     container_name: certbot
23 |     restart: on-failure
24 |     volumes:
25 |       - ./data/certbot/conf:/etc/letsencrypt
26 |       - ./data/certbot/www:/var/www/certbot
27 |     entrypoint: "/bin/sh -c 'trap exit TERM; while :; do certbot renew; sleep 12h & wait $${!}; done;'"
28 | 
29 |   influxdb:
30 |     image: influxdb:1.7.3-alpine
31 |     container_name: tki_influxdb
32 |     restart: on-failure
33 |     volumes:
34 |       - ./run_first_time.sh:/home/run_first_time.sh
35 |       - type: volume
36 |         source: shinyproxy_usage
37 |         target: /var/lib/influxdb
38 |         volume:
39 |           nocopy: true
40 |     networks:
41 |       - tki-net
42 |     ports:
43 |       - 8083:8083
44 |       - 8086:8086
45 | 
46 |   shinyproxy:
47 |     depends_on:
48 |       - influxdb
49 |     image: telethonkids/shinyproxy
50 |     container_name: tki_shinyproxy
51 |     restart: on-failure
52 |     networks:
53 |       - tki-net
54 |     volumes:
55 |       - ./application.yml:/opt/shinyproxy/application.yml
56 |       - /var/run/docker.sock:/var/run/docker.sock
57 |     expose:
58 |       - 8080
59 | 
60 | networks:
61 |   tki-net:
62 |     name: tki-net
63 | 
64 | volumes:
65 |   shinyproxy_usage:
66 | 


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/nginx.conf:
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 1 | worker_processes 1;
 2 | events { worker_connections 1024; }
 3 | 
 4 | http {
 5 |     sendfile on;
 6 |     upstream tki_shinyproxy {
 7 |         server tki_shinyproxy:8080;
 8 |     }
 9 | 
10 |     #### START REMOVE - remove this block of code if SSL certification is not wanted ####
11 |     server {
12 |         listen 80;
13 |         server_name example.org;  #### UPDATE example.org to your domain name ####
14 |         server_tokens off;
15 | 
16 |         location /.well-known/acme-challenge/ {
17 |             root /var/www/certbot;
18 |         }
19 | 
20 |         location / {
21 |             return 301 https://$host$request_uri;
22 |         }
23 |     }
24 |     #### END REMOVE ####
25 | 
26 |     server {
27 |         listen 443 ssl; # listen 80; #### remove "listen 443 ssl; #" statement if SSL certification is not wanted ####
28 |         server_name example.org; #### UPDATE example.org to your domain name ####
29 |         server_tokens off;
30 | 
31 |         #### START REMOVE - remove this block of code if SSL certification is not wanted ####
32 |         ssl_certificate       /etc/letsencrypt/live/example.org/fullchain.pem; #### UPDATE example.org to your domain name ####
33 |         ssl_certificate_key   /etc/letsencrypt/live/example.org/privkey.pem; #### UPDATE example.org to your domain name ####
34 |         include               /etc/letsencrypt/options-ssl-nginx.conf;
35 |         ssl_dhparam           /etc/letsencrypt/ssl-dhparams.pem;
36 |         #### END REMOVE ####
37 | 
38 |         location / {
39 |             proxy_pass         http://tki_shinyproxy;
40 | 
41 |             proxy_http_version 1.1;
42 |             proxy_set_header   Upgrade $http_upgrade;
43 |             proxy_set_header   Connection "upgrade";
44 |             proxy_read_timeout 600s;
45 |             proxy_buffering    off;
46 | 
47 |             proxy_redirect     off;
48 |             proxy_set_header   Host $host;
49 |             proxy_set_header   X-Real-IP $remote_addr;
50 |             proxy_set_header   X-Forwarded-For $proxy_add_x_forwarded_for;
51 |             proxy_set_header   X-Forwarded-Host $server_name;
52 |             proxy_set_header   X-Forwarded-Proto $scheme;
53 |         }
54 |     }
55 | }
56 | 


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/run_first_time.sh:
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 1 | #!/bin/sh
 2 | 
 3 | # Author : Paul Stevenson
 4 | # Create influxdb config file and database for shinyproxy usage statistics
 5 | # only to be run once after the first "docker-compose up -d" on a system
 6 | # run in docker with: docker exec tki_influxdb sh /home/run_first_time.sh
 7 | 
 8 | # influxdb configuration file creation
 9 | influxd config > influxdb.conf
10 | 
11 | # create shinyproxy_usagestats database
12 | influx -execute 'CREATE DATABASE shinyproxy_usage'
13 | 


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/webapp/Dockerfile:
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 1 | FROM rocker/shiny:3.5.1
 2 | 
 3 | RUN apt-get update && apt-get install libcurl4-openssl-dev libnode-dev -y &&\
 4 |     mkdir -p /var/lib/shiny-server/bookmarks/shiny
 5 | 
 6 | # Download and install library
 7 | RUN R -e "install.packages(c('shinydashboard', 'shinyjs', 'V8'))"
 8 | 
 9 | # copy the app to the image
10 | COPY shinyapps /root/app
11 | COPY Rprofile.site /usr/local/lib/R/etc/Rprofile.site
12 | 
13 | # make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
14 | RUN chmod -R 755 /root/app
15 | RUN chmod -R 755 /usr/local/lib/R/etc
16 | 
17 | EXPOSE 3838
18 | 
19 | CMD ["R", "-e", "shiny::runApp('/root/app')"]
20 | 


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/webapp/Rprofile.site:
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1 | local({
2 |    options(shiny.port = 3838, shiny.host = "0.0.0.0")
3 | })
4 | 


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/webapp/shinyapps/app.R:
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 1 | #
 2 | # This is a Shiny web application. You can run the application by clicking
 3 | # the 'Run App' button above.
 4 | #
 5 | # Find out more about building applications with Shiny here:
 6 | #
 7 | #    http://shiny.rstudio.com/
 8 | #
 9 | 
10 | library(shiny)
11 | 
12 | # Define UI for application that draws a histogram
13 | ui <- fluidPage(
14 |    
15 |    # Application title
16 |    titlePanel("Old Faithful Geyser Data"),
17 |    
18 |    # Sidebar with a slider input for number of bins 
19 |    sidebarLayout(
20 |       sidebarPanel(
21 |          sliderInput("bins",
22 |                      "Number of bins:",
23 |                      min = 1,
24 |                      max = 50,
25 |                      value = 30)
26 |       ),
27 |       
28 |       # Show a plot of the generated distribution
29 |       mainPanel(
30 |          plotOutput("distPlot")
31 |       )
32 |    )
33 | )
34 | 
35 | # Define server logic required to draw a histogram
36 | server <- function(input, output) {
37 |    
38 |    output$distPlot <- renderPlot({
39 |       # generate bins based on input$bins from ui.R
40 |       x    <- faithful[, 2] 
41 |       bins <- seq(min(x), max(x), length.out = input$bins + 1)
42 |       
43 |       # draw the histogram with the specified number of bins
44 |       hist(x, breaks = bins, col = 'darkgray', border = 'white')
45 |    })
46 | }
47 | 
48 | # Run the application 
49 | shinyApp(ui = ui, server = server)
50 | 
51 | 


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/webapp/shinylog/placeholder.txt:
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1 | placeholder to sync directory with git


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