Lido to RDF converter

This repository contains a Python library, command line script, and web application to convert LIDO XML files to RDF using X3ML mappings

Installation

The application can be installed with Docker (recommended) or from sources (for development).

With Docker

Pull the current image

docker pull ghcr.io/nfdi4objects/lido-rdf-converter:main

and start a container with docker, or with docker compose and a docker-compose.yml like the one in this repository:

docker run --rm -p 5000:5000 ghcr.io/nfdi4objects/lido-rdf-converter:main

or

docker compose up --force-recreate

From sources

Requires Python >=3.5 and a POSIX compliant operating system. Clone the repository, including its submodules:

git clone --recursive https://github.com/nfdi4objects/lido-rdf-converter.git
cd lido-rdf-converter

Then install dependencies and missing submodules, and enable virtual Python environment:

make deps
. .venv/bin/activate

Usage

Command line client

With Docker the command line client can be called like this:

cat example1.xml | docker run --rm -i ghcr.io/nfdi4objects/lido-rdf-converter:main lido2rdf

Alternatively mount a volume to read and write files:

docker run --rm -v .:/data ghcr.io/nfdi4objects/lido-rdf-converter:main lido2rdf /data/example1.xml

If installed from sources, call ./lido2rdf without any arguments or with --help for help:

usage: lido2rdf [-h] [-o NAME] [-t FORMAT] [-m MAPPING] [LIDO-XML]

Convert LIDO to RDF using X3ML mapping

positional arguments:
  LIDO-XML                       LIDO file or URL (default: -)

options:
  -h, --help                     show this help message and exit
  -o NAME, --output NAME         RDF output file (default: -)
  -t FORMAT, --to FORMAT         RDF output serialization (ttl,nt,json,xml)
  -m MAPPING, --mapping MAPPING  X3ML mapping file (default: defaultMapping.x3ml)

For instance this will convert example1.xml to example1.ttl:

./lido2rdf.py example1.xml -o examle1.ttl

To inspect how an X3ML mapping file is used internally:

./x3ml.py defaultMapping.x3ml

Web application

The web application is made available at http://localhost:5000 by default, if installed via Docker.

Usage if installed from sources is only recommended for development and testing.

If you want to run the web application by script, you have to install some JS scripts first. Therefore, you can use these shell commands:

cd ./static
npm ci
cd ../..

Then start app.py (optionally with argument --port):

python app.py

API

The API has not fully been specified yet an may change.

POST /convert

Convert LIDO/XML with default mapping. Returns RDF in Turtle serialization on success.

LIDO data can be send either via HTTP POST payload or as multipart/form-data file upload:

curl http://127.0.0.1:5000/convert --data-binary @lido.xml --silent
curl http://127.0.0.1:5000/convert -F file=@example.xml --silent

Build and test

To locally build a Docker image for testing:

docker compose build

See Also

• https://github.com/nfdi4objects/lido-schema contains schema files and validation script to check whether an XML file is valid LIDO (included as submodule into directory lido-schema)
• https://github.com/nfdi4objects/lido-examples contains sample LIDO files to be used as test cases

License

MIT License