Implementation of a VSM-dictionary that interfaces with the Uniprot REST API. 

Implementation of a VSM-dictionary that interfaces with the UniProt REST API

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vsm-dictionary-uniprot

Implementation of a VSM-dictionary that interfaces with the Uniprot REST API

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  "description": "Implementation of a VSM-dictionary that interfaces with the Uniprot REST API",

    "test": "mocha \"src/**/*.test.js\" --check-leaks",

    "test": "nyc --reporter=lcov mocha \"src/**/*.test.js\" --check-leaks",

    "build": "webpack --config webpack.config.js"

    "url": "git+https://github.com/vsmjs/vsm-dictionary-uniprot"

[![Travis build status](https://travis-ci.org/vsmjs/vsm-dictionary-uniprot.svg?branch=master)](https://travis-ci.org/vsmjs/vsm-dictionary-uniprot)

[![Build Status](https://travis-ci.com/UniBioDicts/vsm-dictionary-uniprot.svg?branch=master)](https://travis-ci.com/UniBioDicts/vsm-dictionary-uniprot)

[![codecov](https://codecov.io/gh/UniBioDicts/vsm-dictionary-uniprot/branch/master/graph/badge.svg)](https://codecov.io/gh/UniBioDicts/vsm-dictionary-uniprot)

[![npm version](https://img.shields.io/npm/v/vsm-dictionary-uniprot)](https://www.npmjs.com/package/vsm-dictionary-uniprot)

[![Downloads](https://img.shields.io/npm/dm/vsm-dictionary-uniprot)](https://www.npmjs.com/package/vsm-dictionary-uniprot)

[![License](https://img.shields.io/npm/l/vsm-dictionary-uniprot)](#license)

`vsm-dictionary-uniprot` is an implementation 

of the 'VsmDictionary' parent-class/interface (from the package

[`vsm-dictionary`](https://github.com/vsmjs/vsm-dictionary)), that

communicates with [UniProt's](https://www.uniprot.org) 

REST API and translates the provided protein data into a VSM-specific format.

Create a `test.js` file and include this code:

const DictionaryUniprot = require('./DictionaryUniprot');

const dict = new DictionaryUniprot({log: true});

dict.getEntryMatchesForString('tp53', { page: 1, perPage: 10 }, 

      console.log(JSON.stringify(err, null, 4));

      console.log(JSON.stringify(res, null, 4));

Run `npm test`, which runs the source code tests with Mocha.  

If you want to quickly live test the Uniprot API, go to the 

To use a VsmDictionary in Node.js, one can simply run `npm install` and then

use `require()`. But it is also convenient to have a version of the code that

can just be loaded via a &lt;script&gt;-tag in the browser.

Therefore, we included `webpack.config.js`, which is a Webpack configuration 

file for generating such a browser-ready package.

By running `npm build`, the built file will appear in a 'dist' subfolder. 

`<script src="../dist/vsm-dictionary-uniprot.min.js"></script>` in the

Like all VsmDictionary subclass implementations, this package follows

[specification](https://github.com/vsmjs/vsm-dictionary/blob/master/Dictionary.spec.md).

In the next sections we will explain the mapping between the data 

offered by Uniprot's API and the corresponding VSM objects. Useful

- https://www.uniprot.org/help/query-fields

- https://www.uniprot.org/help/uniprotkb_column_names

- https://www.uniprot.org/help/api_queries

- https://www.uniprot.org/help/text-search

Note also that we implement **strict error handling** in the sense that whenever 

we launch multiple parallel queries to Uniprot's REST API (see the functions 

specifications below), if one of them returns an error (either a string or an 

error JSON object response), then the result will be an error object (no matter 

if all the rest of the calls returned proper results). 

If the error response in not a JSON string that we can parse, we formulate the 

error as a JSON object ourselves in the following format:

where the *response* from the server is JSON stringified.

This specification relates to the function:  

If the `options.filter.id` is not properly defined 

or the `https://www.uniprot.org` dictID is included in the 

list of ids used for filtering, `getDictInfos` returns a static object 

- `id`: 'https://www.uniprot.org' (will be used as a `dictID`)

Firstly, if the `options.filter.dictID` is properly defined and in the list of 

dictIDs the `https://www.uniprot.org` dictID is not included, then 

an **empty array** of entry objects is returned.

If the `options.filter.id` is properly defined (with IDs like

`https://www.uniprot.org/uniprot/P12345`) then for each ID (in

		{
		"name": "vsm-dictionary-uniprot",
		"version": "1.0.12",
		"version": "1.0.13",
		"description": "Implementation of a VSM-dictionary that interfaces with the Uniprot REST API",
		@@ -8,3 +8,4 @@ "main": "src/DictionaryUniprot.js",
		"lint": "eslint src test",
		"test": "mocha \"src/*/.test.js\" --check-leaks",
		"test": "nyc --reporter=lcov mocha \"src/*/.test.js\" --check-leaks",
		"coverage": "codecov",
		"build": "webpack --config webpack.config.js"
		@@ -32,15 +33,17 @@ },
		"chai": "^4.2.0",
		"clean-webpack-plugin": "^1.0.1",
		"codecov": "^3.6.5",
		"copy-webpack-plugin": "^5.1.1",
		"eslint": "^5.13.0",
		"html-webpack-plugin": "^3.2.0",
		"js-yaml": ">=3.13.1",
		"lodash": ">=4.17.13",
		"mocha": "^5.2.0",
		"nock": "^9.6.1",
		"nyc": "^15.0.0",
		"terser-webpack-plugin": "^2.3.1",
		"text-transform-loader": "^2.0.0",
		"clean-webpack-plugin": "^1.0.1",
		"copy-webpack-plugin": "^5.1.1",
		"terser-webpack-plugin": "^2.3.1",
		"webpack": "^4.29.0",
		"webpack-cli": "^3.2.1",
		"webpack-dev-server": "^3.1.14",
		"js-yaml": ">=3.13.1",
		"lodash": ">=4.17.13"
		"webpack-dev-server": "^3.1.14"
		},
		@@ -47,0 +50,0 @@ "dependencies": {

Improved metrics

Worsened metrics

		# vsm-dictionary-uniprot

		<!-- badges: start -->
		[![Travis build status](https://travis-ci.org/vsmjs/vsm-dictionary-uniprot.svg?branch=master)](https://travis-ci.org/vsmjs/vsm-dictionary-uniprot)
		[![Build Status](https://travis-ci.com/UniBioDicts/vsm-dictionary-uniprot.svg?branch=master)](https://travis-ci.com/UniBioDicts/vsm-dictionary-uniprot)
		[![codecov](https://codecov.io/gh/UniBioDicts/vsm-dictionary-uniprot/branch/master/graph/badge.svg)](https://codecov.io/gh/UniBioDicts/vsm-dictionary-uniprot)
		[![npm version](https://img.shields.io/npm/v/vsm-dictionary-uniprot)](https://www.npmjs.com/package/vsm-dictionary-uniprot)
		[![Downloads](https://img.shields.io/npm/dm/vsm-dictionary-uniprot)](https://www.npmjs.com/package/vsm-dictionary-uniprot)
		[![License](https://img.shields.io/npm/l/vsm-dictionary-uniprot)](#license)
		<!-- badges: end -->
		@@ -17,2 +19,6 @@

		## Install

		Run: `npm install`

		## Example use
		@@ -19,0 +25,0 @@