Run this

This file depicts example code on how to set up a “Code to run” file for the database connection to use PETDiagnostics. The mothertable and babytable are not yet part of the official cdm therefore they need to added to the cdm.

example for RPostgres

library(PETDiagnostics)
library(CDMConnector)
library(dplyr)

Database connection details

server_dbi<-Sys.getenv(“SERVER_DBI”)
port<-Sys.getenv(“DB_PORT”)
host<-Sys.getenv(“DB_HOST”)
user<-Sys.getenv(“DB_USER”)
password<-Sys.getenv(“DB_PASSWORD”)

to add bigint = “integer” or alternatively bigint = “numeric” is very important

con <- DBI::dbConnect(RPostgres::Postgres(),
dbname = server_dbi,
port = port,
host = host,
user = user,
password = password,
bigint = “integer”)

The name of the schema that contains the OMOP CDM with patient-level data

cdm_database_schema<-Sys.getenv(“DB_CDM_SCHEMA”)

The name of the schema that contains the vocabularies

vocabulary_database_schema<-cdm_database_schema

The name of the schema where results tables will be created

results_database_schema<-Sys.getenv(“DB_WRITE_SCHEMA”)

create cdm reference

cdm <- CDMConnector::cdm_from_con(con,
cdm_schema = cdm_database_schema,
write_schema = results_database_schema)

add your table to the cdm and call it mothertable and babytable (if present)

cdm$mothertable <- dplyr::tbl(con, sql("SELECT * FROM CDM_NAME.TABLE_NAME")) cdm$babytable <- dplyr::tbl(con, sql(“SELECT * FROM CDM_NAME.TABLE_NAME”))