https://github.com/sdsc-ordes/catplus-converters
This repository hosts the CAT+ Zarr converters for different data formats
https://github.com/sdsc-ordes/catplus-converters
rdf rust zarr
Last synced: 2 months ago
JSON representation
This repository hosts the CAT+ Zarr converters for different data formats
- Host: GitHub
- URL: https://github.com/sdsc-ordes/catplus-converters
- Owner: sdsc-ordes
- License: mit
- Created: 2024-10-10T12:24:11.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2025-03-11T16:15:20.000Z (2 months ago)
- Last Synced: 2025-03-11T17:29:18.730Z (2 months ago)
- Topics: rdf, rust, zarr
- Language: Rust
- Homepage: https://swisscatplus.ch
- Size: 186 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Cat+ Zarr Converters
## About
This repository contains all the converters for the different data types in the Cat+ project (Agilent, UV, IR, etc.)
The data types are all in different formats, their data and metadata colluded together. The goal will be to convert the metadata to [an established ontology](https://github.com/sdsc-ordes/catplus-ontology/tree/main), and provide the data in their original files.
## Tools
### converter
The converter parses a json input into an rdf graph and serializes the graph to either turtle or jsonld.
It expects the input to conform to the cat+ ontology and the struct `src/catplus-common/src/models/types.rs`. Example input files are provided in `examples` directory.
#### Usage
The `converter` has four arguments:
- input_type: currently `synth` (see `examples/1-Synth.json`) or `hci` (see `examples/0-HCI.json`)
- inputfile: path to input file (relative to top level of the repo or absolute)
- outputfile: path to output file (relative to top level of the repo or absolute)
- format: rdf output format, currently `turtle` or `jsonld`
The `converter` turns the inputfile into a rdf graph and serializes it to either turtle or jsonld. The serialization is written to the provided outputfile.
Examples
```
just run synth examples/1-Synth.json examples/1-Synth.ttl turtle
just run hci examples/0-HCI.json examples/0-HCI.ttl jsonld
```
### Architecture
The json input is read with `serde_json`: the transformation into rdf is done by the `src/catplus-common` library.
It uses `sophia_rs`. The mapping is triggered by `src/catplus-common/src/models/types.rs` and makes use of the namespaces defined at `src/catplus-common/src/graph/namespaces`.
### Shacl Validation
The rdf graph confirms to the cat+ ontology: https://github.com/sdsc-ordes/catplus-ontology. Currently rust offeres no Shacl Validation Library, but once such a library exists, it would make sense to add a Shacl Validation.
The Shacl Validation can be done manually here: https://www.itb.ec.europa.eu/shacl/any/upload
## Installation guidelines
The repo is setup with nix.
```
git clone [email protected]:sdsc-ordes/catplus-converters.git
cd catplus-converters
cargo build
```
From here on you can work with a just file:
The rust commands can be started via a justfile:
```
just --list
Available recipes:
build *args # Build all crates
default # Default recipe to list all recipes.
format *args # Format all crates
fmt *args # alias for `format`
nix-develop *args # Enter a Nix development shell.
run input_type input_file output_file *args # Run the converter.
test *args # Test all crates
```
### Tests
Run the tests with `just test`: only integration tests have been integrated that ensure that the serialized graph in turtle is isomorphic to an expected turtle serialization of the input data.
### Contribute
The repo is a Poc under heavy development and not yet ready to take contributions.