Docker Config and External DB Not Working

[jorlando-elucid]

Hello,

I am trying to run omero-server inside AWS using an RDS database.

As shown below, I am passing the RDS endpoint as the value for CONFIG_omero_db_host.

However, the container fails to launch with the logs indicating it is looking for the database at postgres:5432 (instead of the db_host I defined above).

Any ideas what I can do to make the container actually use my database url instead of forcing the default of postgres:5432?

[pwalczysko]

with the logs indicating it is looking for the database at postgres:5432 (instead of the db_host I defined above).

Please see the code

omero-server-docker/60-database.sh

Line 31 in ccd8e17

echo "$(date) - postgres:5432 still not reachable, giving up"

which imho will always report that "it is looking for postgres:5432" whatever the truth is - the line in the log seems hardcoded to me.

I am afraid I do not know about the remote postgres server too much, never tried myself.

[pwalczysko]

cc @joshmoore could maybe have more experience with ^^^

[joshmoore]

@jorlando-elucid: Can you confirm that in the server container omero config get omero.db.host shows the value you set? And if so, can you confirm that with psql you can reach 5432 from the server? If so, can you confirm that that database has the expected schema?

[jorlando-elucid]

#98 (comment) Unfortunately, I am in a weird loop. I can't seem to exec into the task until AWS gets a valid health check from the container. However, it doesn't look like we will get a passing health check until this db issue is resolved.

I tried to simulate the issue locally, but the container stops at /startup/60-database.sh just like in AWS.

However, reviewing the script, it seems like a logging anomaly like #98 (comment) pointed out. I am going to look into the AWS networking and validate the connection.

Thanks for helping me track down the error.

[jorlando-elucid]

Just sent over #99 to help with the log message

[jorlando-elucid]

@joshmoore This is a new db. We have not initialized it. I was assuming the container start up logic should be able to do it if the db is not initialized. Is that a bad assumption?

[pwalczysko]

I tried to simulate the issue locally, but the container stops at /startup/60-database.sh just like in AWS.

This means that you never had a running server container locally ? This would be my first step though. I think what @joshmoore is suggesting is to exec into a running server container and check the connection to the db container from there.
True, the server will not start when the DB is not available, and the container might exit (although there is a way to prevent that I believe). Hence, I would first do everything locally (local server container and local DB, ie. just accept the defaults, then, when it is running, exec into the server container and try to connect from there using psql to your remote container with DB in it ?

I am in a weird loop. I can't seem to exec into the task until AWS gets a valid health check from the container. However, it doesn't look like we will get a passing health check until this db issue is resolved.

Not sure I understand that. From what I understood, your step 1 is "have an AWS container where a healthy psql is running with empty DB". Is that wrong ?

the container start up logic should be able to do it if the db is not initialized. Is that a bad assumption?

The intialization of the DB is coming from the OMERO server in the following sense:

omero-server-docker/60-database.sh

Line 45 in ccd8e17

$omego db init --rootpass "$ROOTPASS" --serverdir=OMERO.server

. Hence you need the connection between the DB and the server, and thus the two containers to be working as step 1 afaik.