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Remove server functionality
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ke4 authored Dec 4, 2020
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[![Build Status](https://travis-ci.org/EMBL-EBI-SUBS/json-schema-validator.svg?branch=master)](https://travis-ci.org/EMBL-EBI-SUBS/json-schema-validator)
[![tested with jest](https://img.shields.io/badge/tested_with-jest-99424f.svg)](https://github.com/facebook/jest)

This repository contains a [JSON Schema](http://json-schema.org/) that includes custom extensions of life science data. This package can be used directly or set to run as a node server that receives validation requests and gives back results.
This repository contains a [JSON Schema](http://json-schema.org/) 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](https://nodejs.org/en/) server that receives validation requests and gives back results.
The validation is done using the [AJV](https://github.com/epoberezkin/ajv) library version ^6.0.0 that fully supports the JSON Schema **draft-07**.


## Contents
- [Installation](README.md#install)
- [Installation](README.md#installation)

- [Custom keywords](README.md#custom-keywords)
- [Usage](README.md#usage)

- [Running locally](README.md#running-locally)
- [Custom keywords](README.md#custom-keywords)

- [Validation API](README.md#validation-api)
- [Existing usage of this library](README.md#existing-usage-of-this-library)

- [License](README.md#license)

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## Custom keywords
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 three custom keywords implemented, `graph_restriction`, `isChildTermOf` and `isValidTerm`.
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:

```js
// get all the custom extensions
let { ElixirValidator, GraphRestriction, IsChildTermOf, IsValidTerm]} = require('elixir-jsonschema-validator');
let { ElixirValidator, GraphRestriction, IsChildTermOf, IsValidTerm, isValidTaxonomy]} = require('elixir-jsonschema-validator');
// only use the graph_extension keyword
let validator = new ElixirValidator([GraphRestriction])
```
Expand All @@ -67,7 +68,7 @@ This custom keyword *evaluates if an ontology term is child of another*. This ke
The keyword requires one or more **parent terms** *(classes)* and **ontology ids** *(ontologies)*, both of which should exist in [OLS - Ontology Lookup Service](https://www.ebi.ac.uk/ols).

This keyword works by doing an asynchronous call to the [OLS API](https://www.ebi.ac.uk/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 is a schema, the schema must have the flag: `"$async": true` in it's object root.
Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root.


#### Usage
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The keyword requires the **parent term** and the **ontology id**, both of which should exist in [OLS - Ontology Lookup Service](https://www.ebi.ac.uk/ols).

This keyword works by doing an asynchronous call to the [OLS API](https://www.ebi.ac.uk/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 is a schema, the schema must have the flag: `"$async": true` in it's object root.
Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root.

#### Usage
Schema:
Expand Down Expand Up @@ -136,7 +137,7 @@ JSON object:
This custom keyword *evaluates if a given ontology term url exists in OLS* ([Ontology Lookup Service](https://www.ebi.ac.uk/ols)). 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](https://www.ebi.ac.uk/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 is a schema, the schema must have the flag: `"$async": true` in it's object root.
Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root.

#### Usage
Schema:
Expand All @@ -161,12 +162,12 @@ JSON object:
}
```

### isvalidTaxonomy
### isValidTaxonomy

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](https://www.ebi.ac.uk/ena/taxonomy/rest/any-name/) that will respond with the required information to determine if the term exists or not.
Being an async validation step, whenever used, the schema must have the flag: `"$async": true` in it's object root.
This keyword works by doing an asynchronous call to the [ENA API](https://www.ebi.ac.uk/ena/taxonomy/rest/any-name/<REPLACE_ME_WITH_AXONOMY_TERM>) that will respond with the required information to determine if the term exists or not.
Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root.

#### Usage
Schema:
Expand Down Expand Up @@ -194,190 +195,15 @@ JSON object:
}
```

## Validation API
This validator exposes two endpoints that will accept POST requests: `/validate` for a single stand-alone schema and data object, and `/validateRefs` for a complex schema referencing other schemas and a related data object.

### /validate
The endpoint will expect the body to have the following structure:
```js
{
"schema": {},
"object": {}
}
```
Where the schema should be a valid json schema to validate the object against.

**Example:**
```js
{
"schema": {
"$schema": "http://json-schema.org/draft-07/schema#",

"type": "object",
"properties": {
"alias": {
"description": "A sample unique identifier in a submission.",
"type": "string"
},
"taxonId": {
"description": "The taxonomy id for the sample species.",
"type": "integer"
},
"taxon": {
"description": "The taxonomy name for the sample species.",
"type": "string"
},
"releaseDate": {
"description": "Date from which this sample is released publicly.",
"type": "string",
"format": "date"
}
},
"required": ["alias", "taxonId" ]
},
"object": {
"alias": "MA456",
"taxonId": 9606
}
}
```

### Output

Response with no validation errors:

HTTP status code `200`
```js
[]
```
An example of a validation response with errors:

HTTP status code `200`
```js
[
{
"errors": [
"should have required property 'value'"
],
"dataPath": ".attributes['age'][0].value"
},
{
"errors": [
"should NOT be shorter than 1 characters",
"should match format \"uri\""
],
"dataPath": ".attributes['breed'][0].terms[0].url"
}
]
```
Where *errors* is an array of error messages for a given input identified by its path on *dataPath*. There may be one or more error objects within the response array. An empty array represents a valid validation result.

### API Errors
Sending malformed JSON or a body with either the schema or the submittable missing will result in an API error (the request will not reach the validation).

- When sending malformed JSON:

HTTP status code `400` - Bad Request
```js
{
"errors": "Malformed JSON please check your request body."
}
```
- When any of the required body values is missing:

HTTP status code `422` - Unprocessable Entity
```js
{
"errors": {
"schema": {
"location": "body",
"param": "schema",
"msg": "Required."
},
"object": {
"location": "body",
"param": "object",
"msg": "Required."
}
}
}
```


## Running locally
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

### Prerequisites
To be able to run this project you'll need to have [Node.js](https://nodejs.org/en/about/) and [npm](https://www.npmjs.com/) installed in your machine.
npm is distributed with Node.js which means that when you download Node.js, you automatically get npm installed on your computer.

### Installing

#### Node.js / npm
- Get Node.js: https://nodejs.org/en/ (v8.11.1 LTS)

- If you use [Homebrew](https://brew.sh/) you can install node by doing:
```
brew install node
```

After installation check that everything is correctly installed and which versions you are running:
```
node -v
npm -v
```

#### Project
Clone project and install dependencies:
```
git clone https://github.com/elixir-europe/json-schema-validator.git
cd json-schema-validator
npm install
```

### Running the Tests
```
npm test
```
## Existing usage of this library
You can see how to use this library in this GitHub repository:
[JSON Schema Validator service](https://github.com/EMBL-EBI-SUBS/json-schema-validator).
Please follow the [Geting Started](https://github.com/EMBL-EBI-SUBS/json-schema-validator#getting-started) section
of that repository to set up and execute your own running instance of that validator service into your machine.

### Executing
```
node src/server
```
The node server will run on port **3020** and will expose one endpoint: **/validate**.

#### Startup arguments

- logPath

If provided with a log path argument, the application will write the logs to a file on the specified directory with a 24h rotation. To provide the log path add a `logPath` property after the startup statement:
```
node src/server --logPath=/log/directory/path
```

- pidPath

If provided with a pid file path argument, the application will write the pid into the specified file. If no pid file argument is provided, the application will still create a pid file on the default path: `./server.pid`.
To provide the pid file path add a `pidPath` property after the startup statement:
```
node src/server --pidPath=/pid/file/path/server.pid
```
Note: This is the **file path** and not just the directory it will be written to.

### Executing with Docker
1. Build docker image:
```
docker build -t elixir-jsonschema-validator .
```
2. Run docker image:
```
docker run -p 3020:3020 -d elixir-jsonschema-validator
```
### Development
For development purposes using [nodemon](https://nodemon.io/) is useful. It reloads the application everytime something has changed on save time.
```
nodemon src/server
```
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](README.md#usage) section in this README.

## License
For more details about licensing see the [LICENSE](LICENSE.md).
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