Getting Started / Configuration

The first thing XNAT Populate does is resolve dependencies, so it may appear to be hanging for a couple minutes when running it for the first time.

XNAT Populate is very much a new project, and there is very little error handling. If something goes wrong, the script will likely terminate and print a stack trace out to the command line.

XNAT Populate is a groovy project to push data into an XNAT (XNAT 1.7 required!) instance. Its main uses would be to push a lot of data into an XNAT if the data can be organized according to the desired YAML structure, or to populate a demo/sandbox server with a variety of data. The script uses groovy with dependencies managed by Grape, so the only prerequisite is a recent groovy installation. Then, simply invoke it on the command line by:

groovy PopulateXnat.groovy <parameters>

The script has the following parameters:

Short parameter name Long parameter name Required? Takes argument? Description
-u --user yes yes Specifies the XNAT user to upload data. For full functionality, the user should be an admin, but this is not strictly required to use only parts of the features.
-p --pass yes yes

The password for the user specified above.

-s --url yes yes

The site URL for your XNAT instance to populate.

-d --data yes yes This specifies a text file which defines the data to upload (separated by newlines). See Populate Data for more information about available data. Alternatively, instead of specifying a file, you can enter a comma-separated list of projects here.
-g --config no yes Specifies a YAML file as defined in Site Configuration to set site level properties.
-c --clean no no DANGEROUS. Add this flag to delete preexisting XNAT projects matching the data list. Don't use in production. Also, always back up your data just in case something goes wrong.
-r --refresh-data no no

Semi-dangerous. Add this flag to clear out the data folder on startup. Useful to grab updated copies of data.

-y --refresh-yaml


no Add this flag to delete all YAML files in data folder on startup. Useful to grab updated configuration YAML.
-k --insecure no no Add this flag to ignore SSL errors on https sites. Useful for dev/test environments.
-su --secure-users no no Add this flag to only add existing XNAT users to created projects. Users that are specified in project configurations will not be created (to prevent insecure user accounts).
-e --export-mode no no Add this flag to use XNAT Populate to export data *from* your XNAT to the local file system in a format that it can understand (can then be used to send to a different XNAT).
-w --delay no yes Optional delay (in milliseconds) after each session import. Useful if rapid session imports is degrading performance on the server in constrained memory situations.