@pnatsiavas Here are some responses to your list of questions:
- Did you manually create an empty postgresql database and a database user with permissions to create schemas/tables? Specify that database and user/password in the docker-compose.yml file. When the broadsea-webtools docker container is run for the first time it should automatically create the database schema that includes the source and source_daimon tables. Use a postgres SQL client (e.g. pgadmin) to verify you have a postgresql database and schema that includes those two tables. Also check to make sure that the schema name matches the schema name in your edited source_source_daimon.sql file. The default name for that schema (if you didn’t change it) is “ohdsi”.
Note. Another prerequisite to run the Broadsea OHDSI tools is a OMOP CDM Version 5 database schema populated with OMOP vocabulary & observational data. You will need to create and populate that database manually.
The default name for that schema is “cdm”.
The postresql CDM V5 DDL is here:
https://github.com/OHDSI/CommonDataModel/tree/master/PostgreSQL
A 1k simulated patient CDM V5 dataset that you can load is here:
http://www.ltscomputingllc.com/downloads/
-
Atlas needs the source and source_daimon tables to be populated correctly by the source_source_daimon.sql in order to connect to the database - so this error is probably due to the above issue.
-
Yes. You can use the functionality in Atlas instead of Calypso.
Also, see the “troubleshooting” section at the below URL (scroll down the page) with information on how to review the logs inside the running Broadsea docker container: