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GN Services


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Description

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 - deployed as gn3 user in production

gn-proxy runs in systemd. See

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

gn3 aliases

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!"  ]

genenetwork3 (python3)

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

Notes

System container

systemctl stop genenetwork-development-container
mv /var/guix-containers /export2
systemctl start genenetwork-development-container

The commit that changes the mounts is at

See also


(made with skribilo)