CogStack/CogStack-NiFi

Sample DB docker not populated with data on startup

Closed this issue · 7 comments

chamiw2008 commented

I am deploying the Cogstack on Windows 10 machine for testing.

The Sample BD which is supposed to get populated with following data is empty. Leading to workflows not being run.
patients - structured patient information,
encounters - structured encounters information,
observations - structured observations information,

image

Any thoughts ????

vladd-bit commented

Hello,

I presume that the code you are running is from the master branch. I am not experiencing the same issue, could you try deleting the containers and their volumes and re-creating them ?

Are there any log messages you can share from the db container ?

Thanks

chamiw2008 commented

Hi,

I have deleted and created the containers and volumes many times with the same result.
( I am on Windows 10)

Can you let me know where to find the logs in the db container ?

I see that the two files are copied/accessible from the containers;

      - ../services/pgsamples/db_dump/db_samples-pdf-text-small.sql.gz:/data/db_samples.sql.gz:ro
      - ../services/pgsamples/init_db.sh:/docker-entrypoint-initdb.d/init_db.sh:ro

  -

So I tried to run them from the container (/docker-entrypoint-initdb.d # ./init_db.sh) and got the below error;

Creating database: db_samples and user: test
psql: FATAL:  role "root" does not exist

Thanks,

chamiw2008 commented

Hi,

Below is the only log on the container;

2021-11-23 19:22:47.743 UTC [1] LOG:  listening on IPv4 address "0.0.0.0", port 5432
2021-11-23 19:22:47.743 UTC [1] LOG:  listening on IPv6 address "::", port 5432
2021-11-23 19:22:47.764 UTC [1] LOG:  listening on Unix socket "/var/run/postgresql/.s.PGSQL.5432"
2021-11-23 19:22:47.828 UTC [48] LOG:  database system was shut down at 2021-11-23 19:22:47 UTC
2021-11-23 19:22:47.846 UTC [1] LOG:  database system is ready to accept connections

Thanks,

vladd-bit commented

Hello,

Make sure you are using the latest version of the repository.
The last thing I can suggest is making sure you have read/write/execute permissions on those files.

If you delete the volumes using docker volume rm deploy_samples-vol and recreate the container, could you post the log again using docker logs cogstack-samples-db ?

chamiw2008 commented

Hi,

I think the below was missing in the master branch services.yml

  environment:
      # PG env vars
      - POSTGRES_USER=test
      - POSTGRES_PASSWORD=test

With it the DB was created.
(The tool HeidiSQL has issues showing data from Postgres.)

So will check and come back.

Thanks for the support.

vladd-bit commented

Hello,

If there no further updates I will close the ticket.

chamiw2008 commented