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 identification in the format |
Options
Option |
Description |
---|---|
|
CSV/TSV file path where to write the exported annotations. When not specified, standard output is used. |
|
Exported locale (default is none) |
|
The character separator to be used in the output. When not specified tab character is used. |
|
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 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. |
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