#obo #ontology #validation

bin+lib fastobo-validator

Faultess validation tool for OBO products

9 releases

✓ Uses Rust 2018 edition

0.2.4 Feb 13, 2020
0.2.3 Aug 7, 2019
0.2.2 Jul 23, 2019
0.2.0 Jun 13, 2019
0.1.2 May 25, 2019

#46 in Science

Download history 2/week @ 2019-11-07 17/week @ 2019-11-14 16/week @ 2019-11-21 16/week @ 2019-11-28 8/week @ 2019-12-05 213/week @ 2019-12-12 8/week @ 2019-12-26 1/week @ 2020-01-02 72/week @ 2020-01-09 40/week @ 2020-01-16 1/week @ 2020-01-23 25/week @ 2020-02-13

133 downloads per month

MIT and MPL-2.0 licenses

350KB
9K SLoC

fastobo-validator Star me

Faultess validation tool for OBO products.

TravisCI License Source Binaries Crate Changelog GitHub issues

Overview

fastobo-validator is a command-line tool to validate an OBO file in format version 1.4 against the latest specification.

Setup

fastobo-validator is distributed as a pre-built binary for the following platforms:

Simply download the archive, and unpack the fastobo-validator binary somewhere in your $PATH. For other OS (notably Windows), you'll need to build the binary from source. Make sure to have the Rust compiler installed (check the installation methods) and simply run cargo install fastobo-validator to install the binary in your $CARGO_HOME folder.

Validation

Mandatory

Syntax

The syntax of the OBO format version 1.4 has been made more restrictive compared to the format version 1.2, but files produces by modern tools (such as ROBOT) should already be compliant with this version.

Optional

ISBN validation (-I)

ISBN identifiers embed a validation digit which can be used to validate a given code without querying an external database. Enabling this validation check will process all ISBN-prefixed identifiers for a valid ISBN. It will not check ISBN10 or ISBN13-prefixed identifiers.

Usage

Simply run the binary against one or more OBO files:

$ fastobo-validator go.obo

The validator will then parse and validate each OBO product, and return with a non-null error code if any error was detected, displaying a small report for each error.

Feedback

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker 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 as part of a Master's Degree internship in the BBOP team of the Lawrence Berkeley National Laboratory, under the supervision of Chris Mungall.

Dependencies

~6MB
~121K SLoC