Open logstar opened 1 year ago
I assume this will need to be addressed while working on creating the CNV database for #81 so that might be a good time to implement and review the solution we decide on.
I assume this will need to be addressed while working on creating the CNV database for #81 so that might be a good time to implement and review the solution we decide on.
Thank you for the suggestion. I agree that #81 might be a good place to fix this error permanently. We could discuss further on the solutions in the next API meeting. To avoid blocking the development of CNV databases, any temporary fix could be applied before a permanent fix is decided and implemented.
Regarding options to permanently fix this issue, adding another debian 9
APT repository in db/db.Dockerfile
could also be feasible.
@atlas4213 encountered the following error when building the
db
docker image fromdb/db.Dockerfile
. This error can be reproduced by runningdocker-compose build --no-cache db
.The error is caused by the recent removal of
Debian stretch (9)
from http://apt.postgresql.org/, according to https://wiki.postgresql.org/wiki/Apt.Note that this error does not affect remote DEV/QA/PRD sites, because they use Amazon Relational Database Service (RDS) rather than the
db
docker image to host database servers.To temporarily fix this error:
db
docker image has been built, there is no need to change anything. The image cache should still work when building newdb
docker images.db
docker image has not been built, change the first line ofdb/db.Dockerfile
, https://github.com/PediatricOpenTargets/OpenPedCan-api/blob/0a7046b1dedc7a7b954400edae7a45b4d60a8a98/db/db.Dockerfile#L1, toFROM postgres:12
.The permanent fix of this error is open for discussions. Following are some potential ones:
db/db.Dockerfile
anddb/build_tools/build_db.Dockerfile
. This will require checking PostgreSQL changes from version 11 to 12, to see whether it would be incompatible with any part of theOpenPedCan-api
.curl
installation part indb/db.Dockerfile
. This will require extracting the database downloading procedure, https://github.com/PediatricOpenTargets/OpenPedCan-api/blob/0a7046b1dedc7a7b954400edae7a45b4d60a8a98/db/load_db.sh#L34-L57, to a standalone script. Also, PostgreSQL version 11 only will be supported to November 2023, so the PostgreSQL version needs to be updated before then.cc @sangeetashukla @kelseykeith @ewafula @chinwallaa