inst/doc/a04_DBI_connection_examples.R

In CDMConnector: Connect to an OMOP Common Data Model

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

## ----eval=FALSE---------------------------------------------------------------
# con <- DBI::dbConnect(RPostgres::Postgres(),
#                       dbname = Sys.getenv("CDM5_POSTGRESQL_DBNAME"),
#                       host = Sys.getenv("CDM5_POSTGRESQL_HOST"),
#                       user = Sys.getenv("CDM5_POSTGRESQL_USER"),
#                       password = Sys.getenv("CDM5_POSTGRESQL_PASSWORD"))
# 
# cdm <- cdmFromCon(con,
#                     cdmSchema = Sys.getenv("CDM5_POSTGRESQL_cdmSchema"),
#                     writeSchema = Sys.getenv("CDM5_POSTGRESQL_SCRATCH_SCHEMA"))
# DBI::dbDisconnect(con)

## ----eval=FALSE---------------------------------------------------------------
# con <- DBI::dbConnect(RPostgres::Redshift(),
#                       dbname   = Sys.getenv("CDM5_REDSHIFT_DBNAME"),
#                       host     = Sys.getenv("CDM5_REDSHIFT_HOST"),
#                       port     = Sys.getenv("CDM5_REDSHIFT_PORT"),
#                       user     = Sys.getenv("CDM5_REDSHIFT_USER"),
#                       password = Sys.getenv("CDM5_REDSHIFT_PASSWORD"))
# 
# cdm <- cdmFromCon(con,
#                     cdmSchema = Sys.getenv("CDM5_REDSHIFT_cdmSchema"),
#                     writeSchema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA"))
# DBI::dbDisconnect(con)

## ----eval=FALSE---------------------------------------------------------------
# con <- DBI::dbConnect(odbc::odbc(),
#                       Driver   = "ODBC Driver 18 for SQL Server",
#                       Server   = Sys.getenv("CDM5_SQL_SERVER_SERVER"),
#                       Database = Sys.getenv("CDM5_SQL_SERVER_CDM_DATABASE"),
#                       UID      = Sys.getenv("CDM5_SQL_SERVER_USER"),
#                       PWD      = Sys.getenv("CDM5_SQL_SERVER_PASSWORD"),
#                       TrustServerCertificate="yes",
#                       Port     = 1433)
# 
# cdm <- cdmFromCon(con,
#                     cdmSchema = c("tempdb", "dbo"),
#                     writeSchema =  c("ATLAS", "RESULTS"))
# DBI::dbDisconnect(con)

## ----eval=FALSE---------------------------------------------------------------
# con <- DBI::dbConnect(odbc::odbc(), "SQL")
# cdm <- cdmFromCon(con,
#                     cdmSchema = c("tempdb", "dbo"),
#                     writeSchema =  c("ATLAS", "RESULTS"))
# DBI::dbDisconnect(con)

## ----eval=FALSE---------------------------------------------------------------
# con <- DBI::dbConnect(odbc::odbc(),
#                           SERVER = Sys.getenv("SNOWFLAKE_SERVER"),
#                           UID = Sys.getenv("SNOWFLAKE_USER"),
#                           PWD = Sys.getenv("SNOWFLAKE_PASSWORD"),
#                           DATABASE = Sys.getenv("SNOWFLAKE_DATABASE"),
#                           WAREHOUSE = Sys.getenv("SNOWFLAKE_WAREHOUSE"),
#                           DRIVER = Sys.getenv("SNOWFLAKE_DRIVER"))
# cdm <- cdmFromCon(con,
#                     cdmSchema =  c("OMOP_SYNTHETIC_DATASET", "CDM53"),
#                     writeSchema =  c("ATLAS", "RESULTS"))
# DBI::dbDisconnect(con)

## -----------------------------------------------------------------------------
# con <- DBI::dbConnect(
#   odbc::databricks(),
#   httpPath = Sys.getenv("DATABRICKS_HTTPPATH"),
#   useNativeQuery = FALSE
# )
# 
# cdm <- cdmFromCon(con,
#                   cdmSchema =  "gibleed",
#                   writeSchema = "scratch")
# 
# DBI::dbDisconnect(con)

## ----eval=FALSE---------------------------------------------------------------
# con <- DBI::dbConnect(duckdb::duckdb(),
#                       dbdir=Sys.getenv("CDM5_DUCKDB_FILE"))
# cdm <- cdmFromCon(con,
#                     cdmSchema = "main",
#                     writeSchema = "main")
# DBI::dbDisconnect(con)