obographs-dev

Crate with definitions of Obographs types and I/O functions.

Examples

How to use

Obographs-dev is deployed on crates.io, so including in a project is really easy. Just add the following into your Cargo.toml file:

obographs-dev = "0.2.1"

Note: Check crates.io for the latest version and update 0.2.1 accordingly.

Create an Obographs type

The Obographs elements can be created programatically. For instance, the [obographs::model::Edge] can be created as:

use obographs_dev::model::*;

let edge = Edge {
  sub: String::from("http://purl.obolibrary.org/obo/HP_0001250"),
  pred: String::from("is_a"),
  obj: String::from("http://purl.obolibrary.org/obo/HP_0012638"),
  meta: None,
};

Read an Obographs JSON file

The serde feature is enabled by default, to support reading a JSON file into a [obographs::model::GraphDocument]:

use obographs_dev::model::GraphDocument;

let toy_hpo_json = "tests/test_data/hp.mini.json";
let graph_document = GraphDocument::from_path(toy_hpo_json).expect("Read graph document from file path");

assert_eq!(graph_document.graphs.len(), 1);

Tests and benches

Run the unit, integration, and documentation tests with:

cargo test

The benchmarks can be run with:

cargo bench

Disclaimer

The implementation of the Obographs model is INCOMPLETE. Attributes and components may be missing.