Taxonomy¶
Manage taxonomies: list a summary of the available taxonomies if no option is provided, otherwise download, import or delete a taxonomy.
opal taxonomy <CREDENTIALS> [OPTIONS] [EXTRAS]
Options¶
| Option | Description |
|---|---|
--download DOWNLOAD, -dl DOWNLOAD |
Download a taxonomy from the provided name, in YAML format |
--import-file IMPORT_FILE, -if IMPORT_FILE |
Import a taxonomy from a YAML file in Opal file system. Fail if the taxonomy already exists. |
--delete DELETE, -dt DELETE |
Delete a taxonomy from the provided name |
--force, -f |
Skip taxonomy deletion confirmation |
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¶
List the taxonomies:
opal taxonomy --opal https://opal-demo.obiba.org --user administrator --password password --json
Download a taxonomy in YAML format:
opal taxonomy --opal https://opal-demo.obiba.org --user administrator --password password --download MyTaxo > MyTaxo.yml
Upload a local taxonomy file (in YAML format) into the Opal file system and import it:
opal file --opal https://opal-demo.obiba.org --user administrator --password password --upload /path/to/MyTaxo.yml /home/administrator
opal taxonomy --opal https://opal-demo.obiba.org --user administrator --password password --import-file /home/administrator/MyTaxo.yml
Delete a taxonomy:
opal taxonomy --opal https://opal-demo.obiba.org --user administrator --password password --delete MyTaxo