diff --git a/.dockerignore b/.dockerignore deleted file mode 100644 index 36633d1..0000000 --- a/.dockerignore +++ /dev/null @@ -1,3 +0,0 @@ -examples -node_modules -npm-debug.log \ No newline at end of file diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index c8f6c5f..0000000 --- a/Dockerfile +++ /dev/null @@ -1,11 +0,0 @@ -FROM node:carbon - -# Create app directory -RUN mkdir /app -WORKDIR /app - -ADD src ./src -COPY package*.json ./ - -RUN npm install -CMD ["node", "./src/server.js"] diff --git a/README.md b/README.md index 4e75a7c..40754cb 100644 --- a/README.md +++ b/README.md @@ -2,18 +2,19 @@ [![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) @@ -49,13 +50,13 @@ validator.validate(jsonSchema, jsonObj).then((validationResult) => { ## 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]) ``` @@ -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 @@ -105,7 +106,7 @@ This custom keyword also *evaluates if an ontology term is child of another* and 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: @@ -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: @@ -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: `"$async": true` in it's object root. +This keyword works by doing an asynchronous call to the [ENA API](https://www.ebi.ac.uk/ena/taxonomy/rest/any-name/) that will respond with the required information to determine if the term exists or not. +Being an async validation step, whenever used in a schema, the schema must have the flag: `"$async": true` in its object root. #### Usage Schema: @@ -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). diff --git a/package-lock.json b/package-lock.json index 58472c3..80be8e2 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "elixir-jsonschema-validator", - "version": "1.5.0", + "version": "2.0.0", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -233,6 +233,16 @@ "minimist": "^1.2.0" } }, + "@dabh/diagnostics": { + "version": "2.0.2", + "resolved": "https://registry.npmjs.org/@dabh/diagnostics/-/diagnostics-2.0.2.tgz", + "integrity": "sha512-+A1YivoVDNNVCdfozHSR8v/jyuuLTMXwjWuxPFlFlUapXoGc+Gj9mDlTDDfrwl7rXCl2tNZ0kE8sIBO6YOn96Q==", + "requires": { + "colorspace": "1.1.x", + "enabled": "2.0.x", + "kuler": "^2.0.0" + } + }, "@jest/console": { "version": "24.9.0", "resolved": "https://registry.npmjs.org/@jest/console/-/console-24.9.0.tgz", @@ -622,9 +632,9 @@ "dev": true }, "kind-of": { - 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"integrity": "sha1-lpGEQOMEGnpBT4xS48V06zw+HgU=" + "integrity": "sha1-lpGEQOMEGnpBT4xS48V06zw+HgU=", + "dev": true }, "fast-deep-equal": { "version": "2.0.1", @@ -3060,9 +2837,9 @@ "dev": true }, "fast-safe-stringify": { - "version": "2.0.6", - "resolved": "https://registry.npmjs.org/fast-safe-stringify/-/fast-safe-stringify-2.0.6.tgz", - "integrity": "sha512-q8BZ89jjc+mz08rSxROs8VsrBBcn1SIw1kq9NjolL509tkABRk9io01RAjSaEv1Xb2uFLt8VtRiZbGp5H8iDtg==" + "version": "2.0.7", + "resolved": "https://registry.npmjs.org/fast-safe-stringify/-/fast-safe-stringify-2.0.7.tgz", + "integrity": "sha512-Utm6CdzT+6xsDk2m8S6uL8VHxNwI6Jub+e9NYTcAms28T84pTa25GJQV9j0CY0N1rM8hK4x6grpF2BQf+2qwVA==" }, "fb-watchman": { "version": "2.0.0", @@ -3074,9 +2851,9 @@ } }, "fecha": { - "version": "2.3.3", - "resolved": "https://registry.npmjs.org/fecha/-/fecha-2.3.3.tgz", - "integrity": "sha512-lUGBnIamTAwk4znq5BcqsDaxSmZ9nDVJaij6NvRt/Tg4R69gERA+otPKbS86ROw9nxVMw2/mp1fnaiWqbs6Sdg==" + "version": "4.2.0", + "resolved": "https://registry.npmjs.org/fecha/-/fecha-4.2.0.tgz", + "integrity": "sha512-aN3pcx/DSmtyoovUudctc8+6Hl4T+hI9GBBHLjA76jdZl7+b1sgh5g4k+u/GL3dTy1/pnYzKp69FpJ0OicE3Wg==" }, "file-stream-rotator": { "version": "0.4.1", @@ -3086,20 +2863,6 @@ "moment": "^2.11.2" } }, - 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"integrity": "sha1-+8cfDEGt6zf5bFd60e1C2P2sypE=" + "integrity": "sha1-+8cfDEGt6zf5bFd60e1C2P2sypE=", + "dev": true }, "form-data": { "version": "2.3.3", "resolved": "https://registry.npmjs.org/form-data/-/form-data-2.3.3.tgz", "integrity": "sha512-1lLKB2Mu3aGP1Q/2eCOx0fNbRMe7XdwktwOruhfqqd0rIJWwN4Dh+E3hrPSlDCXnSR7UtZ1N38rVXm+6+MEhJQ==", + "dev": true, "requires": { "asynckit": "^0.4.0", "combined-stream": "^1.0.6", "mime-types": "^2.1.12" } }, - "forwarded": { - "version": "0.1.2", - "resolved": "https://registry.npmjs.org/forwarded/-/forwarded-0.1.2.tgz", - "integrity": "sha1-mMI9qxF1ZXuMBXPozszZGw/xjIQ=" - }, "fragment-cache": { "version": "0.2.1", "resolved": "https://registry.npmjs.org/fragment-cache/-/fragment-cache-0.2.1.tgz", @@ -3143,20 +2908,11 @@ "map-cache": "^0.2.2" } }, - "fresh": { - "version": "0.5.2", - "resolved": "https://registry.npmjs.org/fresh/-/fresh-0.5.2.tgz", - "integrity": "sha1-PYyt2Q2XZWn6g1qx+OSyOhBWBac=" - }, "from": { "version": "0.1.7", "resolved": "https://registry.npmjs.org/from/-/from-0.1.7.tgz", - "integrity": "sha1-g8YK/Fi5xWmXAH7Rp2izqzA6RP4=" - }, - "fs": { - "version": "0.0.1-security", - "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.1-security.tgz", - "integrity": "sha1-invTcYa23d84E/I4WLV+yq9eQdQ=" + "integrity": "sha1-g8YK/Fi5xWmXAH7Rp2izqzA6RP4=", + "dev": true }, "fs.realpath": { "version": "1.0.0", @@ -3184,7 +2940,8 @@ "ansi-regex": { "version": "2.1.1", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "aproba": { "version": "1.2.0", @@ -3205,12 +2962,14 @@ "balanced-match": { "version": "1.0.0", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "brace-expansion": { "version": "1.1.11", "bundled": true, "dev": true, + "optional": true, "requires": { "balanced-match": "^1.0.0", "concat-map": "0.0.1" @@ -3225,17 +2984,20 @@ "code-point-at": { "version": "1.1.0", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "concat-map": { "version": "0.0.1", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "console-control-strings": { "version": "1.1.0", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "core-util-is": { "version": "1.0.2", @@ -3352,7 +3114,8 @@ "inherits": { "version": "2.0.3", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "ini": { "version": "1.3.5", @@ -3364,6 +3127,7 @@ "version": "1.0.0", "bundled": true, "dev": true, + "optional": true, "requires": { "number-is-nan": "^1.0.0" } @@ -3378,6 +3142,7 @@ "version": "3.0.4", "bundled": true, "dev": true, + "optional": true, "requires": { "brace-expansion": "^1.1.7" } @@ -3385,12 +3150,14 @@ "minimist": { "version": "0.0.8", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "minipass": { "version": "2.3.5", "bundled": true, "dev": true, + "optional": true, "requires": { "safe-buffer": "^5.1.2", "yallist": "^3.0.0" @@ -3409,6 +3176,7 @@ "version": "0.5.1", "bundled": true, "dev": true, + "optional": true, "requires": { "minimist": "0.0.8" } @@ -3489,7 +3257,8 @@ "number-is-nan": { "version": "1.0.1", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "object-assign": { "version": "4.1.1", @@ -3501,6 +3270,7 @@ "version": "1.4.0", "bundled": true, "dev": true, + "optional": true, "requires": { "wrappy": "1" } @@ -3586,7 +3356,8 @@ "safe-buffer": { "version": "5.1.2", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "safer-buffer": { "version": "2.1.2", @@ -3622,6 +3393,7 @@ "version": "1.0.2", "bundled": true, "dev": true, + "optional": true, "requires": { "code-point-at": "^1.0.0", "is-fullwidth-code-point": "^1.0.0", @@ -3641,6 +3413,7 @@ "version": "3.0.1", "bundled": true, "dev": true, + "optional": true, "requires": { "ansi-regex": "^2.0.0" } @@ -3684,12 +3457,14 @@ "wrappy": { "version": "1.0.2", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "yallist": { "version": "3.0.3", "bundled": true, - "dev": true + "dev": true, + "optional": true } } }, @@ -3707,7 +3482,8 @@ "get-stream": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-3.0.0.tgz", - "integrity": "sha1-jpQ9E1jcN1VQVOy+LtsFqhdO3hQ=" + "integrity": "sha1-jpQ9E1jcN1VQVOy+LtsFqhdO3hQ=", + "dev": true }, "get-value": { "version": "2.0.6", @@ -3719,6 +3495,7 @@ "version": "0.1.7", "resolved": "https://registry.npmjs.org/getpass/-/getpass-0.1.7.tgz", "integrity": "sha1-Xv+OPmhNVprkyysSgmBOi6YhSfo=", + "dev": true, "requires": { "assert-plus": "^1.0.0" } @@ -3779,35 +3556,17 @@ "integrity": "sha1-8QdIy+dq+WS3yWyTxrzCivEgwIE=", "dev": true }, - "handlebars": { - "version": "4.4.2", - "resolved": "https://registry.npmjs.org/handlebars/-/handlebars-4.4.2.tgz", - "integrity": "sha512-cIv17+GhL8pHHnRJzGu2wwcthL5sb8uDKBHvZ2Dtu5s1YNt0ljbzKbamnc+gr69y7bzwQiBdr5+hOpRd5pnOdg==", - "dev": true, - "requires": { - "neo-async": "^2.6.0", - "optimist": "^0.6.1", - "source-map": "^0.6.1", - "uglify-js": "^3.1.4" - }, - "dependencies": { - "source-map": { - "version": "0.6.1", - "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.6.1.tgz", - "integrity": "sha512-UjgapumWlbMhkBgzT7Ykc5YXUT46F0iKu8SGXq0bcwP5dz/h0Plj6enJqjz1Zbq2l5WaqYnrVbwWOWMyF3F47g==", - "dev": true - } - } - }, "har-schema": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/har-schema/-/har-schema-2.0.0.tgz", - "integrity": "sha1-qUwiJOvKwEeCoNkDVSHyRzW37JI=" + "integrity": "sha1-qUwiJOvKwEeCoNkDVSHyRzW37JI=", + "dev": true }, "har-validator": { "version": "5.1.3", "resolved": "https://registry.npmjs.org/har-validator/-/har-validator-5.1.3.tgz", "integrity": "sha512-sNvOCzEQNr/qrvJgc3UG/kD4QtlHycrzwS+6mfTrrSq97BvaYcPZZI1ZSqGSPR73Cxn4LKTD4PttRwfU7jWq5g==", + "dev": true, "requires": { "ajv": "^6.5.5", "har-schema": "^2.0.0" @@ -3909,36 +3668,23 @@ "whatwg-encoding": "^1.0.1" } }, - "http-errors": { - "version": "1.7.2", - "resolved": "https://registry.npmjs.org/http-errors/-/http-errors-1.7.2.tgz", - "integrity": "sha512-uUQBt3H/cSIVfch6i1EuPNy/YsRSOUBXTVfZ+yR7Zjez3qjBz6i9+i4zjNaoqcoFVI4lQJ5plg63TvGfRSDCRg==", - "requires": { - "depd": "~1.1.2", - "inherits": "2.0.3", - "setprototypeof": "1.1.1", - "statuses": ">= 1.5.0 < 2", - "toidentifier": "1.0.0" - } + "html-escaper": { + "version": "2.0.2", + "resolved": "https://registry.npmjs.org/html-escaper/-/html-escaper-2.0.2.tgz", + "integrity": "sha512-H2iMtd0I4Mt5eYiapRdIDjp+XzelXQ0tFE4JS7YFwFevXXMmOp9myNrUvCg0D6ws8iqkRPBfKHgbwig1SmlLfg==", + "dev": true }, "http-signature": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/http-signature/-/http-signature-1.2.0.tgz", "integrity": "sha1-muzZJRFHcvPZW2WmCruPfBj7rOE=", + "dev": true, "requires": { "assert-plus": "^1.0.0", "jsprim": "^1.2.2", "sshpk": "^1.7.0" } }, - "iconv-lite": { - "version": "0.4.24", - "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.24.tgz", - "integrity": "sha512-v3MXnZAcvnywkTUEZomIActle7RXXeedOR31wwl7VlyoXO4Qi9arvSenNQWne1TcRwhCL1HwLI21bEqdpj8/rA==", - "requires": { - "safer-buffer": ">= 2.1.2 < 3" - } - }, "ignore-by-default": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/ignore-by-default/-/ignore-by-default-1.0.1.tgz", @@ -3998,14 +3744,9 @@ } }, "invert-kv": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/invert-kv/-/invert-kv-1.0.0.tgz", - "integrity": "sha1-EEqOSqym09jNFXqO+L+rLXo//bY=" - }, - "ipaddr.js": { - "version": "1.9.0", - "resolved": "https://registry.npmjs.org/ipaddr.js/-/ipaddr.js-1.9.0.tgz", - "integrity": "sha512-M4Sjn6N/+O6/IXSJseKqHoFc+5FdGJ22sXqnjTpdZweHK64MzEPAyQZyEU3R/KRv2GLoa7nNtg/C2Ev6m7z+eA==" + "version": "2.0.0", + "resolved": "https://registry.npmjs.org/invert-kv/-/invert-kv-2.0.0.tgz", + "integrity": "sha512-wPVv/y/QQ/Uiirj/vh3oP+1Ww+AWehmi1g5fFWGPF6IpCBCDVrhgHRMvrLfdYcwDh3QJbGXDW4JAuzxElLSqKA==" }, "is-accessor-descriptor": { "version": "0.1.6", @@ -4044,7 +3785,8 @@ "is-buffer": { "version": "1.1.6", "resolved": "https://registry.npmjs.org/is-buffer/-/is-buffer-1.1.6.tgz", - 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"wordwrap": { - "version": "0.0.3", - "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-0.0.3.tgz", - "integrity": "sha1-o9XabNXAvAAI03I0u68b7WMFkQc=", - "dev": true - }, "wrap-ansi": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz", @@ -10125,6 +9655,11 @@ "strip-ansi": "^3.0.1" }, "dependencies": { + "ansi-regex": { + "version": "2.1.1", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-2.1.1.tgz", + "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=" + }, "string-width": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/string-width/-/string-width-1.0.2.tgz", @@ -10134,14 +9669,21 @@ "is-fullwidth-code-point": "^1.0.0", "strip-ansi": "^3.0.0" } + }, + "strip-ansi": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz", + "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=", + "requires": { + "ansi-regex": "^2.0.0" + } } } }, "wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - 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}, - "dependencies": { - "camelcase": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-4.1.0.tgz", - "integrity": "sha1-1UVjW+HjPFQmScaRc+Xeas+uNN0=" - }, - "yargs-parser": { - "version": "9.0.2", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-9.0.2.tgz", - "integrity": "sha1-nM9qQ0YP5O1Aqbto9I1DuKaMwHc=", - "requires": { - "camelcase": "^4.1.0" - } - } + } + }, + "yargs-parser": { + "version": "9.0.2", + "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-9.0.2.tgz", + "integrity": "sha1-nM9qQ0YP5O1Aqbto9I1DuKaMwHc=", + "requires": { + "camelcase": "^4.1.0" } } } diff --git a/package.json b/package.json index 4a4e41d..965f541 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "elixir-jsonschema-validator", - "version": "1.6.1", + "version": "2.0.0", "description": "Custom JSON-Schema keywords for Ajv validator and validation service with API", "main": "index.js", "repository": "https://github.com/elixir-europe/json-schema-validator.git", @@ -24,24 +24,11 @@ "license": "Apache-2.0", "dependencies": { "ajv": "^6.10.2", - "amqplib": "^0.5.5", "bluebird": "^3.5.1", - "dnscache": "^1.0.2", - "express": "^4.17.1", - "express-validator": "^6.2.0", - "fs": "0.0.1-security", - "md5": "^2.2.1", - "npid": "^0.4.0", - "path": "^0.12.7", - "rambda": "^1.2.0", - "request": "^2.83.0", - "request-defaults": "^1.2.0", "request-promise": "^4.2.4", "winston": "^3.0.0-rc6", "winston-daily-rotate-file": "^3.2.1", - "yargs": "^11.0.0", - "event-stream": "=3.3.4", - "set-value": "^v3.0.1" + "yargs": "^11.0.0" }, "devDependencies": { "jest": "24.9.0", diff --git a/src/server.js b/src/server.js deleted file mode 100644 index 9b7a7a0..0000000 --- a/src/server.js +++ /dev/null @@ -1,110 +0,0 @@ -const express = require("express"); -const bodyParser = require("body-parser"); -const logger = require("./winston"); -const AppError = require("./model/application-error"); -const { check, validationResult } = require("express-validator/check"); -const path = require('path') - -let ElixirValidator = require('./elixir-validator'); -let GraphRestriction = require('./keywords/graph_restriction'); -let IsChildTermOf = require('./keywords/ischildtermof'); -let IsValidTaxonomy = require('./keywords/isvalidtaxonomy'); - - -const argv = require("yargs").argv; -const npid = require("npid"); - -const app = express(); -const port = process.env.PORT || 3020; -const elixirValidator = new ElixirValidator([GraphRestriction, IsChildTermOf, IsValidTerm, IsValidTaxonomy]); - -app.use(express.static('src/views')); - -// app.use(express.json()); -app.use(bodyParser.json({limit: '50mb'})); -app.use(bodyParser.urlencoded({limit: '50mb', extended: true})); - -app.use(function(req, res, next) { - res.header("Access-Control-Allow-Origin", "*"); - res.header("Access-Control-Allow-Headers", "Origin, X-Requested-With, Content-Type, Accept"); - next(); -}); - -app.use(function(err, req, res, next) { - if (err instanceof SyntaxError && err.status === 400 && "body" in err) { - let appError = new AppError("Received malformed JSON."); - logger.log("info", appError.errors); - res.status(400).send(appError); - } else { - let appError = new AppError(err.message); - logger.log("error", appError.errors); - res.status(err.status).send(appError); - } -}); - -// -- Endpoint definition -- // -app.post("/validate", [ - check("schema", "Required.").exists(), - check("object", "Required.").exists() -],(req, res) => { - const errors = validationResult(req); - if (!errors.isEmpty()) { - return res.status(422).json({ errors: errors.mapped() }); - } else { - logger.log("debug", "Received POST request."); - elixirValidator.validate(req.body.schema, req.body.object).then((output) => { - logger.log("silly", "Sent validation results."); - res.status(200).send(output); - }).catch((err) => { - logger.log("error", err.message); - res.status(500).send(new AppError(err.message)); - }); - } -}); - - -app.get("/validate", (req, res) => { - logger.log("silly", "Received GET request."); - res.send({ - message: "This is the Submissions JSON Schema Validator. Please POST to this endpoint the schema and object to validate structured as showed in bodyStructure.", - bodyStructure: { - schema: {}, - object: {} - }, - repository: "https://github.com/elixir-europe/json-schema-validator" - }); -}); - - -app.listen(port, () => { - logger.log("info", ` -- Started server on port ${port} --`); - if(argv.logPath) { logger.log("info", ` --> Log output: ${argv.logPath}`); } -}); - -// -- For monitoring purposes -- // -const pidPath = argv.pidPath || "./server.pid"; -try { - let pid = npid.create(pidPath); - pid.removeOnExit(); -} catch(err) { - logger.log("error", err); - process.exit(1); -} - -// Handles crt + c event -process.on("SIGINT", () => { - npid.remove(pidPath); - process.exit(); -}); - -// Handles kill -USR1 pid event (monit) -process.on("SIGUSR1", () => { - npid.remove(pidPath); - process.exit(); -}); - -//Handles kill -USR2 pid event (nodemon) -process.on("SIGUSR2", () => { - npid.remove(pidPath); - process.exit(); -}); \ No newline at end of file diff --git a/src/validation-exceptions.js b/src/validation-exceptions.js deleted file mode 100644 index d26f948..0000000 --- a/src/validation-exceptions.js +++ /dev/null @@ -1,11 +0,0 @@ -/** - * Created by rolando on 10/08/2018. - */ - -class NoDescribedBy extends Error {} -class NoFileValidationJob extends Error {} - -module.exports = { - "NoDescribedBy" : NoDescribedBy, - "NoFileValidationJob" : NoFileValidationJob -}; \ No newline at end of file diff --git a/src/views/index.html b/src/views/index.html deleted file mode 100644 index 134acb4..0000000 --- a/src/views/index.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - - - - - - - - - - - - - - - ELIXIR | A distributed infrastructure for life-science information - - - - - - - - - - - - - - -
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Elixir JSON schema validator

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- This page allows you to validate JSON against a JSON schema using the Elixir JSON schema validator. The validator is based on AJV and includes - custom keyword extensions that are relevant for life science data validation. -

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