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Diffstat (limited to 'issues')
| -rw-r--r-- | issues/systems/gn2-time-machines.gmi | 107 |
1 files changed, 107 insertions, 0 deletions
diff --git a/issues/systems/gn2-time-machines.gmi b/issues/systems/gn2-time-machines.gmi index 626eff4..513a91a 100644 --- a/issues/systems/gn2-time-machines.gmi +++ b/issues/systems/gn2-time-machines.gmi @@ -195,3 +195,110 @@ server { ### Setting up GN3 Without gn3 the menu will not show on the main page and you see 'There was an error retrieving and setting the menu. Try again later.' + +GN3 is a separate REST server that has its own dependencies. A bit confusingly it is also a Python module dependency for GN2. So we need to set up both 'routes'. + +First checkout the genenetwork3 repo as gn2 user + +``` +su gn2 +cd /home/gn2 +mkdir -p gn3_production +cd gn3_production +git clone https://github.com/genenetwork/genenetwork3.git +``` + +Check the genenetwork3 README for latest instructions on starting the service as a Guix container. Typically + +``` +guix shell -C --network --expose=$HOME/production/genotype_files/ -Df guix.scm +``` + +where genotype_files is the dir you installed earlier. + +Run it with, for example + +``` +export FLASK_APP="main.py" +flask run --port=8081 +``` + +I.e., the same port as GN2 expects in gn2_settings.py. Test with + +``` +curl localhost:8081/api/version +"1.0" +``` + +Next set up the external API with nginx by adding the following path to above definition: + +``` + location /gn3 { + rewrite /gn3/(.*) /$1 break; + proxy_pass http://127.0.0.1:8081/; + proxy_redirect off; + proxy_set_header Host $host; + } +``` + +and if DNS is correct you should get + +``` +curl gn2-fallback.genenetwork.org/gn3/api/version +"1.0" +``` + +To generate the main menu the server does a request to +$.ajax(gn_server_url +'api/menu/generate/json. On production that is +https://genenetwork.org/api3/api/menu/generate/json which is actually gn3(!) + +``` +curl http://gn2-fallback.genenetwork.org/gn3/api/menu/generate/json +``` + +If this gives an error check the gn3 output log. + +Perhaps obviously, on a production server GN3 should be running as a proper service. + +### Alias service + +There is another GN3 service that resolves wikidata Gene aliases + +``` +su gn2 +cd ~/gn3_production +git clone https://github.com/genenetwork/gn3.git +``` + +follow the instructions in the README and you should get + +``` +curl localhost:8000/gene/aliases/Shh +["Hx","ShhNC","9530036O11Rik","Dsh","Hhg1","Hxl3","M100081","ShhNC"] +``` + +### Authentication proxy + +The proxy also needs to run. + +``` +su gn2 +cd ~/gn3_production +git clone https://github.com/genenetwork/gn-proxy.git +``` + +See README + +### Trouble shooting + +Check the server log for errors from the server. There should be one in /home/gn2/production/tmp/. For example you may see + +``` +ERROR:wqflask:404: Not Found: 7:20AM UTC Aug 20, 2022: http://gn2-fallback.genenetwork.org/api/api/menu/generate/json +``` + +pointing out the setting in gn2_settings.py is wrong. + +Use the console bar of the browse to see what JS error you get. + +If you get CORS errors it is because you are using a server that is not genenetwork.org and this is usually a configuration issue. |