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