## ----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_CDM_SCHEMA"), # writeSchema = Sys.getenv("CDM5_POSTGRESQL_SCRATCH_SCHEMA")) # # DBI::dbDisconnect(con) ## ----eval=FALSE--------------------------------------------------------------- # # library(DatabaseConnector) # connectionDetails <- createConnectionDetails(dbms = "postgresql", # server = Sys.getenv("CDM5_POSTGRESQL_SERVER"), # user = Sys.getenv("CDM5_POSTGRESQL_USER"), # password = Sys.getenv("CDM5_POSTGRESQL_PASSWORD")) # # # con <- connect(connectionDetails) # # cdm <- cdmFromCon(con, # cdmSchema = Sys.getenv("CDM5_POSTGRESQL_CDM_SCHEMA"), # writeSchema = Sys.getenv("CDM5_POSTGRESQL_SCRATCH_SCHEMA")) # # disconnect(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_CDM_SCHEMA"), # writeSchema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA")) # # DBI::dbDisconnect(con) ## ----eval=FALSE--------------------------------------------------------------- # library(DatabaseConnector) # # connectionDetails <- createConnectionDetails(dbms = "redshift", # server = Sys.getenv("CDM5_REDSHIFT_SERVER"), # user = Sys.getenv("CDM5_REDSHIFT_USER"), # password = Sys.getenv("CDM5_REDSHIFT_PASSWORD"), # port = Sys.getenv("CDM5_REDSHIFT_PORT")) # con <- connect(connectionDetails) # # cdm <- cdmFromCon(con, # cdmSchema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"), # writeSchema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA")) # # disconnect(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("cdmv54", "dbo"), # writeSchema = c("tempdb", "dbo")) # # 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--------------------------------------------------------------- # library(DatabaseConnector) # connectionDetails <- createConnectionDetails( # dbms = "sql server", # server = Sys.getenv("CDM5_SQL_SERVER_SERVER"), # user = Sys.getenv("CDM5_SQL_SERVER_USER"), # password = Sys.getenv("CDM5_SQL_SERVER_PASSWORD"), # port = Sys.getenv("CDM5_SQL_SERVER_PORT") # ) # # con <- connect(connectionDetails) # # cdm <- cdmFromCon(con, # cdmSchema = c("cdmv54", "dbo"), # writeSchema = c("tempdb", "dbo")) # # disconnect(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) ## ----eval=FALSE--------------------------------------------------------------- # library(DatabaseConnector) # # connectionDetails <- createConnectionDetails( # dbms = "snowflake", # connectionString = Sys.getenv("SNOWFLAKE_CONNECTION_STRING"), # user = Sys.getenv("SNOWFLAKE_USER"), # password = Sys.getenv("SNOWFLAKE_PASSWORD") # ) # # con <- connect(connectionDetails) # # cdm <- cdmFromCon(con, # cdmSchema = c("OMOP_SYNTHETIC_DATASET", "CDM53"), # writeSchema = c("ATLAS", "RESULTS")) # # disconnect(con) ## ----eval=FALSE--------------------------------------------------------------- # con <- DBI::dbConnect( # odbc::databricks(), # httpPath = Sys.getenv("DATABRICKS_HTTPPATH"), # useNativeQuery = FALSE # ) # # cdm <- cdmFromCon(con, # cdmSchema = "gibleed", # writeSchema = "scratch") # # DBI::dbDisconnect(con) ## ----eval=FALSE--------------------------------------------------------------- # library(DatabaseConnector) # # connectionDetails <- createConnectionDetails( # dbms = "spark", # user = "token", # password = Sys.getenv('DATABRICKS_TOKEN'), # connectionString = Sys.getenv('DATABRICKS_CONNECTION_STRING') # ) # # con <- connect(connectionDetails) # # # cdm <- cdmFromCon(con, # cdmSchema = "gibleed", # writeSchema = "scratch") # # disconnect(con) ## ----eval=FALSE--------------------------------------------------------------- # library(CDMConnector) # con <- DBI::dbConnect(duckdb::duckdb(), # dbdir = eunomiaDir("GiBleed")) # # cdm <- cdmFromCon(con, # cdmSchema = "main", # writeSchema = "main") # # DBI::dbDisconnect(con) ## ----eval=FALSE--------------------------------------------------------------- # library(DatabaseConnector) # connectionDetails <- createConnectionDetails( # "duckdb", # server = CDMConnector::eunomiaDir("GiBleed")) # # con <- connect(connectionDetails) # # cdm <- cdmFromCon(con, # cdmSchema = "main", # writeSchema = "main") # # # disconnect(con)