XNAT to DCAT-AP

This tool queries an XNAT instance and generates DCAT-AP 3.0 metadata. Every XNAT project is considered to be a separate Dataset.

Installation

Download a wheel file from releases and install using pip install. The tool can then be run by running the xnatdcat command from the commandline.

Usage

Basic example: xnatdcat https://xnat.bmia.nl; output will appear at stdout.

The tool supports both public and privat XNAT instances. For authentication, you can either supply a username and/or password at the commandline or use a .netrc file. For more information regarding this, see the XNATpy documentation.

By default, output of the tool is in turtle format at stdout to make for easy piping, but it can be written in a variety of formats to a file, too. For all options, see xnatdcat --help:

usage: xnatdcat [-h] [-u USERNAME] [-p PASSWORD] [-o OUTPUT] [-f FORMAT] [-V] server

This tool generates DCAT from XNAT

positional arguments:
  server                URI of the server to connect to (including http:// or https://)

options:
  -h, --help            show this help message and exit
  -u USERNAME, --username USERNAME
                        Username to use, leave empty to use netrc entry or anonymous login.
  -p PASSWORD, --password PASSWORD
                        Password to use with the username, leave empty when using netrc. If a
                        username is given and no password, there will be a prompt on the console
                        requesting the password.
  -o OUTPUT, --output OUTPUT
                        Destination file to write output to. If not set, the script will print
                        serialized output to stdout.
  -f FORMAT, --format FORMAT
                        The format that the output should be written in. This value references a
                        Serializer plugin in RDFlib. Supportd values are: "xml", "n3", "turtle",
                        "nt", "pretty-xml", "trix", "trig", "nquads", "json-ld" and "hext".
                        Defaults to "turtle".
  -c CONFIG, --config CONFIG
                        Configuration file to use. If not set, will use ~/.xnatdcat/config.toml if
                        it exists.
  -V, --version         show program's version number and exit

Configuration

An example configuration file config.toml is supplied with this project. By default, xnatdcat will look for a configuration file in ~/.xnatdcat/config.toml. The tool will not create the file or folder if it does not exist, you will have to do so manually. If the file does not exist, the example file will be used.

A limited number of properties can be set in the configuration, including the title and name of the xnat (DCAT) catalog and the publisher of the catalog. We are still working on adding more default values for certain DCAT properties to the configuration.

Development

This project uses Hatch as a project manager. After cloning the repository, the development version can be run by hatch run xnatdcat. Hatch will take care of dependencies and all of that.

You can run unit tests by running hatch run test, or get in a shell in the python environment by running hatch shell. Hatch uses whatever Python version is currently loaded. This project is compatible with Python 3.8 and up.

Pull requests are very much welcomed! As long the output remains at least DCAT-AP v3 compliant, we are open to any additions.

Limitations

Currently, only title, description, keywords and PI are set as well as title, description and publisher of the catalogue. There is no Distribution, Dataset Series or anything else. The output does not conform to the Fair Data Point (FDP) specifications yet, but is DCAT-AP 3.0 compliant. The language of the fields also is not set.