18-1 DB: postgres references should now all be Oracle?


Working on setting up my development environment, https://wiki.transmartfoundation.org/display/transmartwiki/2+Dependencies refers as do the folllowing extensions to attaching to a postgres database.

Am I correct that postgres was replaced in the stack by Oracle 12c, and that I should be attaching to the i2b2transmart-db:oracle continer to input data in 18-1-BETA?


I wouldn’t say that POSTGRES was replaced. The goal is to store data in most modern RDBMS instances. Oracle 12c is currently the only one supported under the current quick start release. This is simply because that is the data store that is primarily used in our Lab.


It is on the to-do to make postgres database available. however it is not currently a top priority.


I was just trying to understand that, at the moment, the references in the documentation to postgres are currently being handled by the Oracle DB; and that making it more agnostic is on a roadmap, but that for the moment, when it says "load into postgres" it should be "load into Oracle", and that the mysql DB hanging out in the other container is its own separate beast.


:100: yes (apparently I can’t post less than 20 characters)

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tranSMART platform supports both Oracle and Postgres. Historically the Pharma users prefer Oracle and most research hospitals and academic groups prefer Postgres. We maintain both as separate streams and it is not just a simple swap between the two. But it is also not huge differences. I believe that i2b2 supports both plus another sql db or two but I don’t know which for sure. I will try to look that up, for completeness here. tranSMART 16.2 was Postgres only. I believe that Paul et al made the changes to move it to Oracle. The Foundation has b 16.3 which has both a Postgres stream and an Oracle stream. That is now in final beta, but will be based on original 16.2 and NOT on the Harvard version. The Foundation plans to release v16.4 in a few months that will be full 16.3 plus all the change from Harvard and have both postgres and Oracle support. Our intention is that it can simple drop in to the i2b2/tranSMART configuration with no (or minimal) changes.


The foundation has a policy/mandate to ensure that there is an open technology stack for its platforms. So, it is important to ensure that the project can support open source tools like Postgres, so that adopters have that option.