PaNET build environment

This repo contains tools for working with the Photon and Neutron Experimental Techniques (PaNET) github repository. In particular when building the ontology file PaNET.owl from the various the input files.

There are two main parts:

A script, build-panet, that builds the PaNET. To work, it requires that various software packages are installed.
A 'Dockerfile' script that describes how to build a container image that contains the build-panet script and the software packages it needs.

Using the script directly

The script 'build-panet' uses:

the OBO Robot tool to build the PaNET ontology. Currently, this must be (precisely) v1.8.1: newer versions currently do not work. Note that robot requires that Java is installed.
the git command. This is used to deduce a version number for the ontology. It is possible to avoid a dependency on git by specifying the version explicitly; however, this is not recommended.

The script takes an optional argument: the path of a comma-separated values (csv) input file. The script will create a corresponding OWL file (in RDF/XML) in the same directory. The steps involved are:

Generate an initial set of definitions from the CSV file.
Run a reasoner to deduce more information about terms.
Merge some (fairly constant) information about the ontology itself from the 'PaNET_metadata.ttl' file. This is located in the same directory as the CSV file.

If no argument is given then the path source/PaNET.csv is used. This allows the script to be run from the base directory of the PaNET git repository.

Container image

A container image allows you to build the PaNET ontology without installing any dependencies. You only need the ability to run run a container. This may also be useful when automating, as CI/CD frameworks often support containers.

In order to use the containerised PaNET-build script you must first get the container image onto you computer. There are two main ways of doing this: downloading it and building it yourself. These different approaches are described in the next two sections. If you are not sure, follow the instructions for downloading the image.

Once you have the container image, you can use it to build the PaNET ontology. This is also described below.

Downloading the container image

A pre-build container image is available from this git repo's container registry.

Container images have the label panet-build, with the latest version being panet-build:latest. Therefore, the full reference for the latest container version is gitlab.desy.de:5555/paul.millar/panet-build:latest.

Here is an example command showing how to download the latest image with docker:

docker pull gitlab.desy.de:5555/paul.millar/panet-build:latest

Here is the equivalent command when using podman:

podman pull gitlab.desy.de:5555/paul.millar/panet-build:latest

Building the container image

This step is not necessary if you simply want to build the PaNET ontology. Rather, this information is useful if you wish to enhance the build process in a way that requires additional tools.

This git repo contains the Dockerfile file that contains instructions for building the container image.

The image may be built using a standard procedure. The following instructions show how to build the image and tag it panet-build:latest if the repo is the current directory.

Here is the command for docker:

docker build . -t panet-build

and for podman:

podman build . -t panet-build

Using the container image

By default, the container image expects the PaNET git repository to be available as the /work directory within the container image. Typically, this is achieved by "mounting" the PaNET git repository directory (on the host computer) at this location.

This may be done by explicitly specifying the git location.

A typical command with docker is:

docker run -v ~/git/PaNET/:/work --rm -it panet-build

... or with podman:

podman run -v ~/git/PaNET/:/work --rm -it panet-build

Often, the current directory is the PaNET git repository's base directory. In this case, then a somewhat simplified version of the command may be used.

Here is a complete example, showing how to check out PaNET and use docker to build the ontology:

cd ~/git git clone https://github.com/ExPaNDS-eu/ExPaNDS-experimental-techniques-ontology PaNET cd PaNET docker run -v $PWD/:/work --rm -it panet-build

Here is the same example but using podman instead:

cd ~/git git clone https://github.com/ExPaNDS-eu/ExPaNDS-experimental-techniques-ontology PaNET cd PaNET podman run -v $PWD/:/work --rm -it panet-build

The container accepts argument and passes these to the script. Therefore, it is possible to specify a target CSV file, similar to running the script directly. Note that the build process assumes that the ontology metadata is available as the file PaNET_metadata.ttl in the same directory as the source CSV file.

Specifying an alternative source file may be useful, under some specific circumstances. However, the reader is encouraged to edit the PaNET.csv file directly and to use git to manage those changes.