adding key commands, server information, and contribution to document…

…ation

source/contribute-to-the-guide.md

@@ -1,3 +1,3 @@
 # Documentation
 
-Guidance on how the guide is set-up and how to contribute
+This documentation was created using sphinx and is hosted on readthedocs. The repository for this documentation can be found [here](https://github.com/l-gorman/legume-choice-docs). The markdown files which contain the content can all be found in the `source` directory. To add new sections to the documentation, add a new markdown (or RST) file to the source directory, and refer to the file in the toctree (found in the `index.rst` file) to ensure it is included in the table of contents.

source/key-vm-commands.md

@@ -1,3 +1,11 @@
 # Key Commands for Virtual Machine
 
-A cheatsheet for running, stopping, and restarting processes on the legumeCHOICE virtual machine.
+This document contains key information to get started working with the legumeCHOICE VM. It includes some information about where important files are stored as well as a cheatsheet for running, stopping, and restarting processes.
+
+A repository has been created for two of the main server files, this can be found [here](https://github.com/l-gorman/legume-choice-conf).
+
+To restart the NGINX server enter the command `systemctl restart nginx`
+
+To restart the python daemon enter the command `systemctl restart legume_choice_data_process.service`, followed by the command `systemctl daemon-reload`.
+
+To restart the API, enter the command `pm2 restart ~ubuntu/legumeCHOICE/api/server.js`.

source/nginx.md

@@ -1,3 +1,9 @@
 # Server
 
-LegumeCHOICE uses an NGINX server.
+LegumeCHOICE uses an NGINX server. A proxy server has been configured to pass requests to the [API](api.md). All of the configuration for the NGINX server can be found in the default sites-enabled. On the legumeCHOICE VM, this file can be found at:
+
+`/etc/nginx/sites-available/default`
+
+The SSL certificate was obtained using letsencrypt, using this [guide](https://www.digitalocean.com/community/tutorials/how-to-secure-nginx-with-let-s-encrypt-on-ubuntu-20-04).
+
+Files for [public data](public-data.md) and [private data](administrators.md) are made available using NGINX auto-index. The administrator files are secured with HTTP basic authentication. See [here](https://docs.nginx.com/nginx/admin-guide/security-controls/configuring-http-basic-authentication/) for how authentication was implemented, and how to add new users/passwords.