From the XNAT point of view, there’s no difference between nginx with SSL and without: in both cases the request comes from the proxy to port 8080 (presuming you haven’t changed the default port on Tomcat). I’ve attached two different nginx configurations:
I can’t really help you with getting Let’s Encrypt itself set up. I previously managed Let’s Encrypt-issued certs using certbot, but switched to using acme.sh because it’s the only solution I could get working that supports issuing wildcard certificates for my DNS provider. I never had any real trouble getting certbot to work so if you can use that to manage your certificates I think that would help.
Computational Imaging Laboratory
Washington University School of Medicine
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