Annotations Export

Export the variable annotations of one or all tables of a project. This can be used to backup annotations, that can be restored using Annotations Import.

opal export-annot <RESOURCE> <CREDENTIALS> [OPTIONS] [EXTRAS]

Arguments

Argument Description
RESOURCE Resource identification in the format <datasource>[.<table>]. Each project has a datasource which is identified by the project’s name.

Options

Option Description
--output OUTPUT, -out OUTPUT CSV/TSV file path where to write the exported annotations. When not specified, standard output is used.
--locale LOCALE, -l LOCALE Exported locale (default is none)
--separator SEPARATOR, -s SEPARATOR The character separator to be used in the output. When not specified tab character is used.
--taxonomies TAXONOMIES [TAXONOMIES ...], -tx TAXONOMIES [TAXONOMIES ...] The list of taxonomy names of interest (default is any that are found in the variable attributes).

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.

Example

Export annotations of the Mlstr_area taxonomy from a specific table:

opal export-annot --opal https://opal-demo.obiba.org --user administrator --password password CLSA --taxonomies Mlstr_area --out /tmp/clsa-area.tsv