The following connection examples are provided for reference.
RedshiftRedshift is almost identical to Postgres.
SQL ServerUsing odbc with SQL Server requires driver setup described here. Note, you’ll likely need to download the ODBC Driver for SQL Server.
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)
The connection to SQL Server can be simplified by configuring a DSN. See here for instructions on how to set up the DSN.If we named it “SQL”, our connection is then simplified to.
SnowflakeWe can use the odbc package to connect to snowflake.
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)
Note, as with SQL server we could set up a DSN to simplify this connection as described here for windows and here for macOS.
DuckdbDuckdb is an in-process database. We use the duckdb package to connect.
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