Crate obographs_dev

obographs-dev

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

Typically, the library should be used with serde feature enabled to support parsing Obographs JSON files.

Therefore, the following should be added into Cargo.toml file:

obographs-dev = {version = '0.2.1', features = ["serde"]}

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

Examples

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

With serde feature enabled, we can read a JSON file into a [obographs::model::GraphDocument] by running:

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 tests with:

cargo test --features serde

The benchmarks can be run with:

cargo bench --features serde

Disclaimer

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

Modules

model

The module with Obographs types.