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:
- required input files. Eido adds
requied_files, which allows a schema author to specify which attributes must point to files that exist.
- optional input files.
filesspecifies which attributes point to files that may or may not exist.
- project and sample validation. Eido validates project attributes separately from sample attributes.
- schema imports. Eido adds an
importssection for schemas that should be validated prior to this schema
- 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
- Use eido to validate data from the command line
- Use eido to validate data from Python
- Write your own schema
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.