Export RDS (R)

Export in RDS format in Opal file system. A RDS file contains a single serialized R object, which will be a tibble and that can be read in R using base::readRDS().

opal export-r-rds <CREDENTIALS> <OPTIONS> [EXTRAS]

Options

Option Description
--datasource DATASOURCE, -d DATASOURCE Datasource name
--tables TABLES [TABLES ...], -t TABLES [TABLES ...] The list of tables to be exported
--incremental -i Incremental export
--identifiers ID_MAPPING, -id ID_MAPPING Entity ID mapping name
--id-name ID_NAME, -in ID_NAME ID column name (optional)
--output OUTPUT, -out OUTPUT Output RDS file name on the Opal file system

Credentials

Authentication can be done by username/password credentials OR by personal access token OR by certificate/private key pair (two-way SSL authentication).

Option Description
--opal OPAL, -o OPAL Opal server base url
--user USER, -u USER Credentials auth: user name (requires a password)
--password PASSWORD, -p PASSWORD Credentials auth: user password (requires a user name)
--token TOKEN, -tk TOKEN Token auth: User access token
--ssl-cert SSL_CERT, -sc SSL_CERT Two-way SSL auth: certificate/public key file (requires a private key)
--ssl-key SSL_KEY, -sk SSL_KEY Two-way SSL auth: private key file (requires a certificate)

Extras

Option Description
-h, --help Show the command help’s message.
--verbose, -v Verbose output.
--json, -j Pretty JSON formatting of the response.

Example

Export table from opal-data to a RDS file:

opal export-r-rds --opal https://opal-demo.obiba.org --user administrator --password password --datasource CNSIM --tables CNSIM1 --output /tmp/cnsim1.rds