Annotations Import¶
Import the variable annotations of one or more tables. This can be used to restore annotations that were backed up using Annotations Export.
opal import-annot <CREDENTIALS> [OPTIONS] [EXTRAS]
Options¶
| Option | Description |
|---|---|
--input INPUT, -in INPUT |
CSV/TSV input file, typically the output of the export-annot command (default is stdin) |
--locale LOCALE, -l LOCALE |
Destination annotation locale (default is none) |
--separator SEPARATOR, -s SEPARATOR |
Separator char for CSV/TSV format (default is the tabulation character) |
--destination DESTINATION, -d DESTINATION |
Destination project name (default is the one(s) specified in the input file) |
--tables TABLES [TABLES ...], -t TABLES [TABLES ...] |
The list of tables which variables are to be annotated (defaults to all that are found in the input file) |
--taxonomies TAXONOMIES [TAXONOMIES ...], -tx TAXONOMIES [TAXONOMIES ...] |
The list of taxonomy names of interest (default is any that is found in the input file) |
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¶
Import some annotations to a specified table:
opal import-annot --user administrator --password password --destination Study2 --tables datasetA --input /tmp/area-annotations.tsv