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First make sure to have a stable guix checkout. E.g.
gn3@tux01:~/production/gn-proxy$ /home/wrk/opt/guix-pull/bin/guix pull -p ~/opt/guix-pull
In addition to gn1 and gn2 we have 3 running gn3 services:
gn-proxy runs in systemd. See
https://github.com/genenetwork/gn-proxy/blob/master/.guix-run
https://github.com/genenetwork/gn-proxy/blob/master/extra/guix-gn-proxy.service
Test with
curl localhost:8080/version
{"version":"0.2.1"}
curl https://genenetwork.org/gn3-proxy/version
{"version":"0.2.1"}
To deploy by hand use
su gn3 alias guix=~/opt/guix/bin/guix gn3@tux01:~/production/gn-proxy source .guix-deploy raco pkg install --auto env TMPDIR=/home/gn3/tmp SQL_USER=*** SQL_PASSWORD=*** racket -L info server/rest.rkt
https://github.com/genenetwork/gn3/blob/master/.guix-run
https://github.com/genenetwork/gn3/blob/master/etc/gn3-aliases.service
Test with
curl http://localhost:8000/gene/aliases/BRCA2 ["FACD","FAD","FANCD","BROVCA2","FAD1","FANCD1","BRCC2","GLM3","PNCA2","XRCC11"] curl http://localhost:8000/ [ "Hello GeneNetwork3!" ] curl https://genenetwork.org/gn3 [ "Hello GeneNetwork3!" ] curl https://luna.genenetwork.org/gn3/ [ "Hello GeneNetwork3!" ]
If the menu does not load, this is the culprit. It should be an external API link.
gn3@tux02:~/production/genenetwork3$ env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/opt/guix-gn3/bin/guix shell -C -D --network --expose=/home/gn2/production/genotype_files/ -f guix.scm -- gunicorn --bind 0.0.0.0:8087 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app
Test with
curl localhost:8087/api/version "1.0" curl localhost:8087/api/menu/generate/json ... curl https://genenetwork.org/api3/api/version "1.0" curl https://genenetwork.org/api3/api/menu/generate/json tomato curl -L https://luna.genenetwork.org/api3/version "1.0"
note the menu is more recent GN3.
On epysode:
http://mars.genenetwork.org/gn3/api/version "1.0" http://gn2-fallback.genenetwork.org/gn3/api/menu/generate/json tomato
We track services now on
https://rabbit.genenetwork.org/sheepdog/index.html
systemctl stop genenetwork-development-container mv /var/guix-containers /export2 systemctl start genenetwork-development-container
The commit that changes the mounts is at
https://github.com/genenetwork/genenetwork-machines/commit/8ce668562b0443ed7eb5b22225692f6f4383ea89