eido Build Status Coverage Status PEP compatible

Introduction

Eido is a validation tool for PEPs based on JSON Schema. The PEP specification defines a formal structure for organizing project and sample metadata, and eido provides a way to validate if data complies with that specification. Eido extends the JSON Schema vocabulary with PEP-specific features, like required input files.

Why do we need eido?

A PEP consists of metadata describing a set of items called samples. The metadata is divided into two-components: 1) sample-specific attributes; and 2) project attributes, which apply to all samples. A PEP follows a formal specification for formatting and organizing this data. Projects that follow the PEP specification can be read by a variety of PEP-compatible tools, which may require specific sample or project attributes. Eido is used to validate these specific required attributes.

JSON Schema is a vocabulary that allows you to annotate and validate JSON documents. It's great for validating JSON documents, but alone it cannot validate a PEP, which has powerful portability features that go beyond a simple JSON document, so we require additional capability to validate it. Eido extends JSON Schema to add this capability, along with other features for validating sample metadata listed below.

PEP-specific validation features

An eido schema is written using the JSON Schema vocabulary, plus a few additional features:

  1. required input files. Eido adds requied_files, which allows a schema author to specify which attributes must point to files that exist.
  2. optional input files. files specifies which attributes point to files that may or may not exist.
  3. project and sample validation. Eido validates project attributes separately from sample attributes.
  4. schema imports. Eido adds an imports section for schemas that should be validated prior to this schema
  5. automatic multi-value support. Eido validates successfully for singular or plural sample attributes for strings, booleans, and numbers. This accommodates the PEP subsample_table feature.

How to use eido


What does 'eido' mean?

Eidos is a Greek term meaning form, essence, or type (see Plato's Theory of Forms). Schemas are analogous to forms, and eido tests claims that an instance is of a particular form.