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