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’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. |
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