Using CDM tables for Achilles (ATLAS)

@Ajit_Londhe @Chris_Knoll @t_abdul_basser

Hi, would like to check if the cdm and results schema should be located in the same database as the webapi schema i.e OHDSI. Looking at the R-code for running the Achilles analysis, the database isn’t specified so I’m a bit confused as to how Achilles knows which database to find the cdm and results schema, especially if the cdm and results schema are locates in a different database from the webapi schema:

library(Achilles)
connectionDetails <- createConnectionDetails(
  dbms="redshift", 
  server="server.com", 
  user="secret", 
  password='secret', 
  port="5439")

achilles(connectionDetails, 
  cdmDatabaseSchema = "cdm5_inst", 
  resultsDatabaseSchema="results",
  vocabDatabaseSchema = "vocab",
  numThreads = 1,
  sourceName = "My Source Name", 
  cdmVersion = "5.3.0",
  runHeel = TRUE,
  runCostAnalysis = TRUE)

Also,

  1. should the cdm and results schema be created by the default user (i.e. postgres)?
  2. what are the privileges to grant ohdsi_admin_user and ohdsi_app_user with regards to this schemas? Looking at the above, it seems that we have to change the user and password to that of ohdsi_app_user, or ohdsi_admin_user which means that we first need to allow them to access the tables…

I’ve already imported the SynPUF CDM tables into a schema called cdm, under a database called CDM – all of these were done by the default user ‘Postgres’. I haven’t granted any privileges on the cdm table/schema/database to the ohdsi_admin_user or ohdsi_app_user at the moment. If I have used the wrong location or login then should I delete these tables, login as ohdsi_admin user and create them in the correct location and with the correct rights?

Thanks in advance and sorry for the spam :blush: ~
Hui Xing