nginx unable to retrieve schema.json

[lbeckman314]

Hi All! Thanks for all the effort put into this helm project! Using your instructions we were able to get a Gen3 local deployment via Helm up and running with custom TLS certs.

@bwalsh, @matthewpeterkort, @jawadqur

Issue Encountered

We are running into a small bug regarding schema.json, specifically with retrieving it during run time from the data portal.

Logs and Info

Judging by the rexproxy logs nginx is unable to find schema.json due to it not being in the expected directory within the portal deployment:

2023/03/02 22:08:42 [error] 18#18: *29 open() "/usr/share/nginx/html/data/schema.json" failed (2: No such file or directory), client: 10.42.0.125, server: , request:
"GET //data/schema.json HTTP/1.0", host: "aced-training.compbio.ohsu.edu", referrer: "https://aced-training.compbio.ohsu.edu/_root"
10.42.0.125 - - [02/Mar/2023:22:08:42 +0000] "GET //data/schema.json HTTP/1.0" 404 153 "https://aced-training.compbio.ohsu.edu/_root" "Mozilla/5.0 (Macintosh; Intel M
ac OS X 10.15; rv:109.0) Gecko/20100101 Firefox/110.0" "10.42.0.34"

Successful fetching of the data schema upon building the data portal:

INFO: Running schema and relay for non-workspace bundle

> cloud_portal@0.1.0 schema
> node ./data/getSchema

Fetching http://revproxy-service/api/v0/submission/getschema
Fetching http://revproxy-service/api/v0/submission/_dictionary/_all
All done!

schema.json is successfully written to the /data-portal/data directory:

root@portal-deployment-7dcd4c8446-8gk7d:/data-portal/data# ls
config           dictionaryHelper.js       getSchema.js  gqlHelper.js.njk  parameters.js   schema.json
dictionary.json  dictionaryHelper.test.js  getTexts.js   gqlSetup.js       schema.graphql  utils.js

root@portal-deployment-7dcd4c8446-8gk7d:/data-portal/data# ls -alt schema.json
-rw-r--r-- 1 root root 5624461 Mar  2 22:11 schema.json

schema.json is not written or copied to the the nginx directory where it can then be served in the data portal:

ls -alt /usr/share/nginx/html/data/schema.json
ls: cannot access '/usr/share/nginx/html/data/schema.json': No such file or directory

Current Fix

Manually copying the file from /data/schema.json to the the /usr/share/nginx/html/data/ directory solves the issue.