So I have the functionality in the script to upload the certificate and private-key however, Fortigate functionality doesn't let you overwrite the current certificate, and even if it did you would have to remove and then re-add ssl functionality to the specific service if you are overwriting the certificate.
 
Since this is the case, I'm going to also have to write functionality to change the certificates of rules, VPN portals, Virtual servers, either into the same script or into a separate script.  Let me know if anyone is interested so far.

adam_smith@sundance.org
So I have the functionality in the script to upload the certificate and private-key however, Fortigate functionality doesn't let you overwrite the current certificate, and even if it did you would have to remove and then re-add ssl functionality to the specific service if you are overwriting the certificate.
 
Since this is the case, I'm going to also have to write functionality to change the certificates of rules, VPN portals, Virtual servers, either into the same script or into a separate script.  Let me know if anyone is interested so far.

I would be interested in the script.
 
I have been trying to figure this out for awhile but im not much of a scripter.
You would think this would be an API they would have given all the rage of DevOPs these days.

there doesn't seem to be a way for me to put the file here but I am planning to put it up on github so that as it evolves people can get the latest versions.  I also am planning on releasing it with an apache v2 license, so don't worry about changing it for your own purposes and any contributions/suggestions would help.  Sorry for taking so long to post it.  I was trying to add a config file functionality that is present in the code but is not fully working yet.  However all the command line options all work.  This is a python script and relies on  fortiosapi so you will have to use that.  It was written with python3 in mind so it may or may not be reverse compatible with python2.  I actually think that it won't be reverse compatible because of the configuration file library I used changed the syntax for the library name when it moved over to python3.  With that in mind here is what I have currently.
 
I am also planning on making it compatible with pypi so you can just do a pip install, but that isn't all in place yet.  I'll post the link as soon as I get it on github.

Fortinet could just add support for LetsEncrypt into FortiOS, the ACME protocol is open source and anybody can write a client for it.
 
Apart from that, Fortinet already uses python in FortiOS, they could use certbot...