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//! *Faultless AST for Open Biomedical Ontologies.* //! //! [](https://travis-ci.org/fastobo/fastobo/branches) //! [](https://codecov.io/gh/fastobo/fastobo) //! [](https://choosealicense.com/licenses/mit/) //! [](https://github.com/fastobo/fastobo) //! [](https://crates.io/crates/obofoundry) //! [](https://docs.rs/fastobo) //! [](https://github.com/fastobo/fastobo/blob/master/README.md) //! [](https://github.com/fastobo/fastobo/issues) //! //! ## Overview //! //! This library provides a mostly-complete implementation of the //! [OBO flat file format 1.4](http://owlcollab.github.io/oboformat/doc/obo-syntax.html). //! //! * **Data structures** - `fastobo` provides a complete owned AST for the //! OBO language, with constructors and covenience traits where applicable. //! There is a plan to provide borrowed data structures as well, to be able //! to build a view of an OBO document from borrowed data. //! * **Parsing** - The parser is implemented using [pest](http://pest.rs/), //! and is reexported from the [`fastobo-syntax`](https://crates.io/crates/fastobo-syntax) //! crate. Most structures implement the [`FromPair`](./parser/trait.FromPair.html) //! trait which allows to build a data structure from a stream of pest tokens. //! * **Errors** - All functions in that crate that return a `Result` will //! always use the `Error` struct defined in the `error` module. Errors //! reported by pest are very meaningful, and can give the exact location //! of a syntax error encountered by the parser. //! * **Semantics** - This library exports specific traits that can be used //! to edit an OBO syntax tree with the semantics expected in the format //! guide: mapping identifiers to URLs, adding default namespaces, or //! expanding entity frames using `treat-xrefs` macros. //! //! *Warning: this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html), //! but the API is likely to change a lot before the release of a stable 1.0.* //! //! //! ## Usage //! //! Add `fastobo` to the `[dependencies]` sections of your `Cargo.toml` manifest: //! ```toml //! [dependencies] //! fastobo = "0.1.0" //! ``` //! //! The [`OboDoc`](./ast/struct.OboDoc.html) struct acts as the root of the AST. //! Use [`OboDoc::from_stream`](ast/struct.OboDoc.html#method.from_stream) to load //! an OBO document from a [`BufRead`](https://doc.rust-lang.org/std/io/trait.BufRead.html) //! implementor (use [`std::io::BufReader`](https://doc.rust-lang.org/std/io/struct.BufReader.html) //! if needed to adapt from a raw stream): //! //! ```rust //! extern crate fastobo; //! extern crate ureq; //! //! fn main() { //! let response = ureq::get("http://purl.obolibrary.org/obo/ms.obo").call(); //! let mut reader = std::io::BufReader::new(response.into_reader()); //! //! match fastobo::ast::OboDoc::from_stream(&mut reader) { //! Ok(doc) => println!("Number of MS entities: {}", doc.entities().len()), //! Err(e) => panic!("Could not parse the Mass-Spec Ontology: {}", e), //! } //! } //! ``` //! //! //! ## See also //! //! * [`fastobo-py`](https://pypi.org/project/fastobo/): Idiomatic Python bindings to this crate. //! //! //! ## Feedback //! //! Found a bug ? Have an enhancement request ? Head over to the //! [GitHub issue tracker](https://github.com/fastobo/fastobo/issues) of the project if //! you need to report or ask something. If you are filling in on a bug, please include as much //! information as you can about the issue, and try to recreate the same bug in a simple, easily //! reproducible situation. //! //! //! ## About //! //! This project is currently being developed by [Martin Larralde](https://github.com/althonos) //! as part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the //! [Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of //! [Chris Mungall](http://biosciences.lbl.gov/profiles/chris-mungall/). #![allow(dead_code, unused_imports)] #[macro_use] extern crate failure; #[macro_use] extern crate opaque_typedef_macros; extern crate fastobo_syntax; #[cfg(feature = "memchr")] extern crate memchr; extern crate opaque_typedef; extern crate pest; extern crate url; #[cfg(test)] extern crate textwrap; #[macro_use] pub mod parser; pub mod ast; pub mod error; pub mod share; pub mod visit; pub mod ext;