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’s personal 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 |
Output pretty-print JSON |
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