Import Stata (R)¶
Import a Stata file, to be found in Opal file system, using R.
opal import-r-stata <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 Stata file to import on the Opal file system |
--locale LOCALE, -l LOCALE |
Language code to be associated to labels |
--type TYPE, -ty TYPE |
Entity type (default is Participant) |
--idVariable IDVARIABLE, -iv IDVARIABLE |
Stata variable that provides the entity ID. If not specified, first variable 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’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¶
Import table from RobotChicken Stata file in opal-data datasource:
opal import-r-stata --opal https://opal-demo.obiba.org --user administrator --password password --destination opal-data --locale en --path /home/administrator/RobotChicken.dta