Import RDS (R)
Import a RDS file, to be found in Opal file system, using R. A RDS file contains a single serialized R object, which is expected to be a tibble and that can be produced in R using base::saveRDS().
opal import-r-rds <CREDENTIALS> <OPTIONS> [EXTRAS]
Options
Option |
Description |
---|---|
|
Destination datasource name |
|
The list of tables to be imported (defaults to all) |
|
Incremental import |
|
Name of the ID mapping |
|
ID mapping policy:
required : each identifiers must be mapped prior importation (default),ignore : ignore unknown identifiers,generate : generate a system identifier for each unknown identifier. |
|
Path to the RDS file to import on the Opal file system |
|
Entity type (default is Participant) |
|
tibble’s column name that provides the entity ID. If not specified, first column values are considered to be the entity identifiers. |
|
Merge imported data dictionary with the destination one (default is false, i.e. data dictionary is overridden). |
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 server base url |
|
Credentials auth: user name (requires a password) |
|
Credentials auth: user password (requires a user name) |
|
Token auth: user’s personal access token |
|
Two-way SSL auth: certificate/public key file (requires a private key) |
|
Two-way SSL auth: private key file (requires a certificate) |
Extras
Option |
Description |
---|---|
|
Show the command help’s message. |
|
Verbose output. |
|
Output pretty-print JSON |
Example
Import table from CNSIM1 RDS file in CNSIM project:
opal import-r-rds --opal https://opal-demo.obiba.org --user administrator --password password --destination CNSIM --path /home/administrator/CNSIM1.rds