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 DESTINATION, -d DESTINATION Destination datasource name
--tables TABLES [TABLES ...], -t TABLES [TABLES ...] The list of tables to be imported (defaults to all)
--incremental -i Incremental import
--identifiers IDENTIFIERS, -id IDENTIFIERS Name of the ID mapping
--policy POLICY, -po POLICY
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 PATH -pa PATH Path to the RDS file to import on the Opal file system
--type TYPE, -ty TYPE Entity type (default is Participant)
--idVariable IDVARIABLE, -iv IDVARIABLE tibble’s column name that provides the entity ID. If not specified, first column values are considered to be the entity identifiers.
--merge, -mg 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 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

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