This repository is archived now in favour of enhanced and supported version biovalidator. Please use biovalidator repository for all future uses and references.
This repository contains a JSON Schema validator that includes custom extensions of life science data. This package contains only a library for schema validation. You can use it as a dependency to set up and run it as a Node.js server that receives validation requests and gives back results. The validation is done using the AJV library version ^6.0.0 that fully supports the JSON Schema draft-07.
npm install elixir-jsonschema-validator
let { ElixirValidator} = require('elixir-jsonschema-validator');
let jsonSchema = {
$schema: "http://json-schema.org/draft-07/schema#",
type:"object",
properties: {
alias: {
description: "A sample unique identifier in a submission.",
type: "string"
}
},
required: ["alias"]
};
let jsonObj = { alias : "MTB1"};
let validator = new ElixirValidator();
validator.validate(jsonSchema, jsonObj).then((validationResult) => {
console.log(validationResult.validationState)
for ( let errors of validationResult.validationErrors) {
console.log(errors.userFriendlyMessage)
}
});The AJV library supports the implementation of custom json schema keywords to address validation scenarios that go beyond what json schema can handle.
This validator has four custom keywords implemented: graph_restriction, isChildTermOf, isValidTerm and isValidTaxonomy.
Pick the custom keywords you want to support and add them to the Elixir validator:
// get all the custom extensions
let { ElixirValidator, GraphRestriction, IsChildTermOf, IsValidTerm, isValidTaxonomy]} = require('elixir-jsonschema-validator');
// only use the graph_extension keyword
let validator = new ElixirValidator([GraphRestriction])This custom keyword evaluates if an ontology term is child of another. This keyword is applied to a string (CURIE) and passes validation if the term is a child of the term defined in the schema. The keyword requires one or more parent terms (classes) and ontology ids (ontologies), both of which should exist in OLS - Ontology Lookup Service.
This keyword works by doing an asynchronous call to the OLS API that will respond with the required information to know if a given term is child of another.
Being an async validation step, whenever used in a schema, the schema must have the flag: "$async": true in its object root.
Schema:
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "http://schema.dev.data.humancellatlas.org/module/ontology/5.3.0/organ_ontology",
"$async": true,
"properties": {
"ontology": {
"description": "A term from the ontology [UBERON](https://www.ebi.ac.uk/ols/ontologies/uberon) for an organ or a cellular bodily fluid such as blood or lymph.",
"type": "string",
"graph_restriction": {
"ontologies" : ["obo:hcao", "obo:uberon"],
"classes": ["UBERON:0000062","UBERON:0000179"],
"relations": ["rdfs:subClassOf"],
"direct": false,
"include_self": false
}
}
}
}JSON object:
{
"ontology": "UBERON:0000955"
}This custom keyword also evaluates if an ontology term is child of another and is a simplified version of the graph_restriction keyword. This keyword is applied to a string (url) and passes validation if the term is a child of the term defined in the schema. The keyword requires the parent term and the ontology id, both of which should exist in OLS - Ontology Lookup Service.
This keyword works by doing an asynchronous call to the OLS API that will respond with the required information to know if a given term is child of another.
Being an async validation step, whenever used in a schema, the schema must have the flag: "$async": true in its object root.
Schema:
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$async": true,
"properties": {
"term": {
"type": "string",
"format": "uri",
"isChildTermOf": {
"parentTerm": "http://purl.obolibrary.org/obo/PATO_0000047",
"ontologyId": "pato"
}
}
}
}JSON object:
{
"term": "http://purl.obolibrary.org/obo/PATO_0000383"
}This custom keyword evaluates if a given ontology term url exists in OLS (Ontology Lookup Service). It is applied to a string (url) and passes validation if the term exists in OLS. It can be aplied to any string defined in the schema.
This keyword works by doing an asynchronous call to the OLS API that will respond with the required information to determine if the term exists in OLS or not.
Being an async validation step, whenever used in a schema, the schema must have the flag: "$async": true in its object root.
Schema:
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$async": true,
"properties": {
"url": {
"type": "string",
"format": "uri",
"isValidTerm": true
}
}
}JSON object:
{
"url": "http://purl.obolibrary.org/obo/PATO_0000383"
}This custom keyword evaluates if a given taxonomy exists in ENA's Taxonomy Browser. It is applied to a string (url) and passes validation if the taxonomy exists in ENA. It can be aplied to any string defined in the schema.
This keyword works by doing an asynchronous call to the ENA API that will respond with the required information to determine if the term exists or not.
Being an async validation step, whenever used in a schema, the schema must have the flag: "$async": true in its object root.
Schema:
{
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "Is valid taxonomy expression.",
"$async": true,
"properties": {
"value": {
"type": "string",
"minLength": 1,
"isValidTaxonomy": true
}
}
}JSON object:
{
"metagenomic source" : [ {
"value" : "wastewater metagenome"
} ]
}You can see how to use this library in this GitHub repository: JSON Schema Validator service. Please follow the Getting Started section of that repository to set up and execute your own running instance of that validator service into your machine.
If you would like to create your own service/repository using this library, you can check the code in that repository and/or you can also check the Usage section in this README.
For more details about licensing see the LICENSE.