Update README.md docs

Author: nuno-agostinho

README.md

@@ -5,16 +5,16 @@ Visit our website at https://compbio.imm.medicina.ulisboa.pt!
 This project uses:
 - [Docker Compose][] to manage multiple Docker containers
 - [Nginx][] as a reverse proxy (i.e. to redirect URLs), to serve SSL
-certificates and to show a public folder
+certificates and to show a [public](nginx/public) folder
 - [ShinyProxy][] to run R/Shiny and Python apps via Docker
 - [Celery][] to run background tasks via a job queue system
   - [Flower][] to monitor Celery and to send jobs to Celery via its REST API
   - [Redis][] to serve as message broker for celery
 - [Prometheus][] and [Grafana][] to log and visualise ShinyProxy and Celery data
 - [RStudio Server][] to test code on-the-fly
-- [Plausible][] for (multiple) website analytics
-  - [Postgres][] database for Plausible's user data
-  - [Clickhouse][] database for Plausible's analytics
+- [Plausible][] analytics to gather traffic metrics of multiple websites
+  - [Postgres][] database (Plausible's user data)
+  - [Clickhouse][] database (Plausible's analytics)
 
 [Docker Compose]: https://docs.docker.com/compose/
 [ShinyProxy]: https://shinyproxy.io
@@ -56,8 +56,8 @@ to avoid restarting the whole server
 ### Next steps
 
 - [Add and update apps in ShinyProxy](shinyproxy)
-- [Monitor website analytics](plausible)
-- [Renew SSL certificates](nginx)
+- [Monitor website analytics with Plausible](plausible)
+- [Renew SSL certificates in Nginx](nginx)
 
 ## Relevant assets
 
@@ -68,7 +68,7 @@ Asset                                           | Description
 [`shinyproxy/application.yml`][application.yml] | ShinyProxy configuration (including Shiny apps)
 [`shinyproxy/templates`](shinyproxy/templates)  | ShinyProxy custom HTML files
 [`celery/tasks.py`](celery/tasks.py)            | Celery tasks
-[`public`](public)                              | Publicly available data downloadable at [`/public`][public]
+[`public`](nginx/public)                        | Publicly available data downloadable at [`/public`][public]
 
 [application.yml]: shinyproxy/application.yml
 [nginx.conf]: nginx/nginx.conf

docker-compose.yml

@@ -10,7 +10,7 @@ services:
     volumes:
       - ./nginx:/etc/nginx
       - /etc/ssl/imm:/etc/nginx/certs:ro
-      - ./public:/public:ro
+      - ./nginx/public:/public:ro
     depends_on:
       - shinyproxy
       - flower
@@ -52,14 +52,14 @@ services:
       - GF_AUTH_ANONYMOUS_HIDE_VERSION=true
 
   redis:
+    image: redis:6-alpine
     container_name: redis
-    image: redis:alpine
     ports:
       - 6379:6379
 
   prometheus:
-    container_name: prometheus
     image: prom/prometheus
+    container_name: prometheus
     volumes:
       - ./prometheus:/etc/prometheus:ro
       - prometheus-data:/prometheus

nginx/README.md

@@ -1,4 +1,12 @@
-# CompBio App Server - Nginx configuration
+# Nginx
+
+[Nginx][] is the orchestrator of the server behind-the-scenes and responsible
+for the following:
+
+- Reverse proxy (i.e. URL redirection)
+- Serve SSL certificates
+- [Public](public) folder: all data in this folder is available to be browsed
+and downloaded at [/public](https://compbio.imm.medicina.ulisboa.pt/public)
 
 ## SSL certificate renewal
 
@@ -7,7 +15,7 @@ certificates need to be renewed frequently (e.g. every year). To do so:
 
 1. Update the SSL certificate files
 
-2. In case the filename of the SSL certificate changes, open the file
+2. In case the filename of the SSL certificate changes, open
 [`nginx.conf`][nginx.conf] and replace the path to the certificates (in
 `ssl_certificate` and `ssl_certificate_key`)
 

public/README.md renamed to nginx/public/README.md

@@ -1,17 +1,15 @@
-# CompBio App Server - Plausible analytics
+# Plausible analytics
 
 [Plausible](plausible.io) is an [open-source][], [privacy-focused][] web
-analytics tool that provides website traffic metrics via an interactive
-dashboard. This project runs the self-hosted version of Plausible.
+analytics tool that provides traffic metrics for multiple websites via an
+interactive dashboard. This project runs the self-hosted version of Plausible.
 
 [open-source]: https://plausible.io/open-source-website-analytics
 [privacy-focused]: https://plausible.io/privacy-focused-web-analytics
 
-Plausible presents (unique) visitor numbers, total page views, session duration
-and other useful metrics. All of these metrics are anonymously collected as
-aggregated data without using cookies (or other persistent identifiers) and do
-not include personally identifiable information. As stated by Plausible's
-[data policy][]:
+All of Plausible metrics (e.g., visitor numbers, total page views and session
+duration) are anonymously aggregated without cookies, thus avoiding individual
+tracing. As stated by their [data policy][]:
 
 > By using Plausible, you don’t need to have any GDPR, CCPA or PECR prompts and
 you don’t need a complex privacy policy about your use of analytics and

plausible/README.md

@@ -1,12 +1,12 @@
-# CompBio App Server - ShinyProxy configuration
+# ShinyProxy
 
-## Add new apps to ShinyProxy
-
-[ShinyProxy][] deploys Shiny and Python apps via Docker images. Put simply, you
-will need to:
+[ShinyProxy][] is open-source and allows to deploy R/Shiny and Python apps via
+Docker images.
 
 [ShinyProxy]: https://shinyproxy.io
 
+## Add new apps to ShinyProxy
+
 ### 1. [Create a Docker image of your app][deploying]
 
 I suggest uploading your Docker image to DockerHub and then pulling it from the

shinyproxy/README.md

@@ -30,7 +30,7 @@
     	<div class="row">
             <div class="col-lg-3 col-md-4 col-sm-6" th:each="app: ${apps}" style="min-height: 140px;">
                 <h1><a th:href="@{/app/}+${app.id}" th:text="${app.displayName == null} ? ${app.id} : ${app.displayName}"></a></h1>
-                <p th:if="${app.description != null}" th:text="${app.description}" ></p>
+                <p th:text="${app.description}" ></p>
             </div>
         </div>
         <hr></hr>