cbioportal-api-client - npm Package Compare versions

Comparing version 0.1.1 to 0.2.0

dist/index.js

@@ -14,9 +14,3 @@ 'use strict';
 });
-exports.convertResponse = convertResponse;
-exports.default = CbioPortal;
 
-var _bluebird = require('bluebird');
-
-var _bluebird2 = _interopRequireDefault(_bluebird);
-
 var _requestPromise = require('request-promise');
@@ -26,3 +20,3 @@
 
-var _csvtojson = require('csvtojson');
+var _utils = require('./utils');
 
@@ -32,33 +26,8 @@ function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
 /**
- * @module cbioportal-api-client
- */
-
-/**
- * Converts tab delimited responses to JSON format
- *
- * @param  {string} response TSV string
- * @return {Promise}          Resolves with the response JSON
- */
-function convertResponse(response) {
-  var responseConverter = new _csvtojson.Converter({
-    delimiter: '\t',
-    flatKeys: true
-  });
-
-  return new _bluebird2.default(function (resolve) {
-    responseConverter.fromString(response, function (err, result) {
-      if (err) {
-        throw new Error(err);
-      }
-
-      return resolve(result);
-    });
-  });
-}
-
-/**
  * cbioPortal API Object Prototype. Used as the object prototype
  * when creating an API client object via the module factory method.
  *
- * @see Use {@link module:cbioportal-api-client~CbioPortal|CbioPortal()} for object creation.
+ * @memberOf module:cbioportal-api-client
+ * @alias module:cbioportal-api-client~cbioPortal
+ * @see Use {@link module:cbioportal-api-client|CbioPortal()} for object creation.
  * @type {Object}
@@ -98,3 +67,3 @@ */
     return (0, _requestPromise2.default)(requestOpts).then(function (response) {
-      return convertResponse(response);
+      return (0, _utils.convertResponse)(response);
     });
@@ -107,3 +76,4 @@ },
    * @instance
-   * @return {Promise} resolves with JSON data
+   * @return {Promise} See fullfills/rejects
+   * @fulfills {Array} response data converted from TSV to JSON
    */
@@ -118,3 +88,4 @@ getTypesOfCancer: function getTypesOfCancer() {
    * @instance
-   * @return {Promise} resolves with JSON data
+   * @return {Promise} See fullfills/rejects
+   * @fulfills {Array} response data converted from TSV to JSON
    */
@@ -132,3 +103,4 @@ getCancerStudies: function getCancerStudies() {
    * @param  {string} query.cancer_study_id Cancer study ID
-   * @return {Promise(data)} resolves with JSON data
+   * @return {Promise} See fullfills/rejects
+   * @fulfills {Array} response data converted from TSV to JSON
    */
@@ -151,4 +123,4 @@ getGeneticProfiles: function getGeneticProfiles(_ref) {
    * @param  {string} query.cancer_study_id Cancer study ID
-   * @return {Promise(data)}
-   */
+   * @return {Promise}
+  * @fulfill JSON formatted response   */
   getCaseLists: function getCaseLists(_ref2) {
@@ -164,7 +136,8 @@ var cancer_study_id = _ref2.cancer_study_id;
    * @instance
+   * @param {Object} query
    * @param  {string} options.case_set_id        A unique ID used to identify the case list ID in subsequent interface calls. This is a human readable ID. For example, "gbm_all" identifies all cases profiles in the TCGA GBM study.
    * @param  {Array.<string>|string} options.genetic_profile_id One or more genetic profile IDs
    * @param  {Array.<string>|string} options.gene_list          One or more genes, specified as HUGO Gene Symbols or Entrez Gene IDs
-   * @return {Promise(data)}
-   */
+   * @return {Promise}
+  * @fulfill JSON formatted response   */
   getProfileData: function getProfileData(_ref3) {
@@ -197,2 +170,4 @@ var case_set_id = _ref3.case_set_id;
  *
+ * @module cbioportal-api-client
+ * @see {@link module:cbioportal-api-client~cbioPortal|cbioPortal}
  * @param {Object} config Configuration options object.
@@ -211,2 +186,4 @@ * @param {Boolean} config.includeRaw Include the raw TSV response
   });
-}
+}
+
+exports.default = CbioPortal;

lib/index.js

@@ -8,38 +8,12 @@ /**
 
-import Promise from 'bluebird';
 import Request from 'request-promise';
-import { Converter } from 'csvtojson';
+import { convertResponse } from './utils';
 
 /**
- * @module cbioportal-api-client
- */
-
-/**
- * Converts tab delimited responses to JSON format
- *
- * @param  {string} response TSV string
- * @return {Promise}          Resolves with the response JSON
- */
-export function convertResponse (response) {
-  const responseConverter = new Converter({
-    delimiter: '\t',
-    flatKeys: true
-  });
-
-  return new Promise(resolve => {
-    responseConverter.fromString(response, (err, result) => {
-      if (err) {
-        throw new Error(err);
-      }
-
-      return resolve(result);
-    });
-  });
-}
-
-/**
  * cbioPortal API Object Prototype. Used as the object prototype
  * when creating an API client object via the module factory method.
  *
- * @see Use {@link module:cbioportal-api-client~CbioPortal|CbioPortal()} for object creation.
+ * @memberOf module:cbioportal-api-client
+ * @alias module:cbioportal-api-client~cbioPortal
+ * @see Use {@link module:cbioportal-api-client|CbioPortal()} for object creation.
  * @type {Object}
@@ -76,3 +50,4 @@ */
    * @instance
-   * @return {Promise} resolves with JSON data
+   * @return {Promise} See fullfills/rejects
+   * @fulfills {Array} response data converted from TSV to JSON
    */
@@ -87,3 +62,4 @@ getTypesOfCancer () {
    * @instance
-   * @return {Promise} resolves with JSON data
+   * @return {Promise} See fullfills/rejects
+   * @fulfills {Array} response data converted from TSV to JSON
    */
@@ -101,3 +77,4 @@ getCancerStudies () {
    * @param  {string} query.cancer_study_id Cancer study ID
-   * @return {Promise(data)} resolves with JSON data
+   * @return {Promise} See fullfills/rejects
+   * @fulfills {Array} response data converted from TSV to JSON
    */
@@ -118,4 +95,5 @@ getGeneticProfiles ({ cancer_study_id }) {
    * @param  {string} query.cancer_study_id Cancer study ID
-   * @return {Promise(data)}
-   */
+   * @return {Promise}
+
+* @fulfill JSON formatted response   */
   getCaseLists ({ cancer_study_id }) {
@@ -129,7 +107,9 @@ return this.get('CaseLists', { cancer_study_id });
    * @instance
+   * @param {Object} query
    * @param  {string} options.case_set_id        A unique ID used to identify the case list ID in subsequent interface calls. This is a human readable ID. For example, "gbm_all" identifies all cases profiles in the TCGA GBM study.
    * @param  {Array.<string>|string} options.genetic_profile_id One or more genetic profile IDs
    * @param  {Array.<string>|string} options.gene_list          One or more genes, specified as HUGO Gene Symbols or Entrez Gene IDs
-   * @return {Promise(data)}
-   */
+   * @return {Promise}
+
+* @fulfill JSON formatted response   */
   getProfileData ({ case_set_id, genetic_profile_id, gene_list }) {
@@ -159,2 +139,4 @@ return this.get('ProfileData', { case_set_id, genetic_profile_id, gene_list });
  *
+ * @module cbioportal-api-client
+ * @see {@link module:cbioportal-api-client~cbioPortal|cbioPortal}
  * @param {Object} config Configuration options object.
@@ -164,3 +146,3 @@ * @param {Boolean} config.includeRaw Include the raw TSV response
  */
-export default function CbioPortal ({ includeRaw = false } = {}) {
+function CbioPortal ({ includeRaw = false } = {}) {
   return Object.assign(Object.create(cbioPortal), {
@@ -170,1 +152,3 @@ includeRaw
 }
+
+export default CbioPortal;

package.json

 {
   "name": "cbioportal-api-client",
-  "version": "0.1.1",
+  "version": "0.2.0",
   "description": "cBio Portal API client with promises and response parsing",
   "main": "dist/index.js",
+  "bin": {
+    "cbioportal-api-client": "./bin/cbioportal-api-client.js"
+  },
   "scripts": {
-    "build": "npm run clean:dist && babel lib -d dist",
+    "build": "npm run docs && npm run clean:dist && babel lib -d dist",
+    "build:dev": "nodemon -w lib --exec \"npm run docs && npm run clean:dist && babel lib -d dist\"",
     "clean": "npm run clean:dist && npm run clean:coverage",
@@ -14,3 +18,3 @@ "clean:dist": "rimraf dist",
     "dev": "nodemon -w lib -w test --exec \"npm run -s lint && npm run -s test:dev\"",
-    "docs": "jsdoc2md --src lib/**/*.js -t docs/README.md.hbs -l JavaScript > README.md",
+    "docs": "jsdoc2md --src \"lib/**/*.js\" -t docs/README.md.hbs -d 2 --partial \"./docs/partials/**/*.hbs\" --separators  -l JavaScript > README.md",
     "lint": "eslint lib",
@@ -37,2 +41,3 @@ "precommit": "npm run docs",
     "babel-eslint": "^5.0.0-beta6",
+    "babel-plugin-transform-es2015-modules-commonjs": "^6.4.5",
     "blue-tape": "^0.1.11",
@@ -43,3 +48,3 @@ "coveralls": "^2.11.6",
     "isparta": "^4.0.0",
-    "jsdoc": "git+https://github.com/jsdoc3/jsdoc.git",
+    "jsdoc": "^3.4.0",
     "jsdoc-to-markdown": "^1.3.3",
@@ -58,6 +63,8 @@ "nock": "^5.2.1",
     "bluebird": "^3.1.1",
+    "commander": "^2.9.0",
     "csvtojson": "^0.5.1",
     "in-publish": "^2.0.0",
+    "lodash": "^4.0.0",
     "request-promise": "^2.0.0"
   }
 }

README.md

 # cBio Portal API Client
 [![Build Status](https://img.shields.io/circleci/project/nathanmarks/cbioportal-api-client/master.svg?style=flat-square)](https://circleci.com/gh/nathanmarks/cbioportal-api-client) [![Coverage Status](https://img.shields.io/coveralls/nathanmarks/cbioportal-api-client/master.svg?style=flat-square)](https://coveralls.io/github/nathanmarks/cbioportal-api-client?branch=master)
 
-[cBio Portal API](http://www.cbioportal.org/web_api.jsp) client. Parses tab separated responses into JSON format and works in node and also in the browser via a module loader such as Webpack.
+[cBio Portal API](http://www.cbioportal.org/web_api.jsp) client. Parses tab separated responses into JSON format. Works in node and in the browser via a module loader such as [Webpack](http://webpack.github.io).
 
+This library can be used programatically or via the command line.
+
+#### Installation
+
+```bash
+$ npm install cbioportal-api-client --save
+```
+
+#### Programmatic Usage
+
+[API Reference](#api-reference)
+
+```javascript
+import CbioPortal from 'cbioportal-api-client';
+
+const cbioPortal = CbioPortal();
+
+cbioPortal.getCancerStudies()
+  .then(response => {
+    console.log(response); // Prints array of cancer studies returned from API
+  });
+
+cbioPortal.getGeneticProfiles({ cancer_study_id: 'gbm_tcga' })
+  .then(response => {
+    console.log(response); // Prints array of genetic profiles returned from the 'gbm_tcga' study
+  });
+```
+
+#### Command Line Usage
+
+**Note:** Requires node.
+
+```bash
+# global install to use anywhere
+$ npm install -g cbioportal-api-client
+
+# print usage info using --help
+$ cbioportal-api-client --help
+
+  Usage: cbioportal-api-client [options] [command]
+
+
+  Commands:
+
+    getCancerStudies               get cancer study meta-data
+    getTypesOfCancer               get clinical cancer types
+    getGeneticProfiles [options]   get genetic profile data for a cancer study.
+    getCaseLists [options]         get case lists stored for a specific cancer study.
+    getProfileData [options]       get genomic profile data for one or more genes.
+
+  You can get usage info for specific commands using [command] --help
+
+  Options:
+
+    -h, --help             output usage information
+    -V, --version          output the version number
+    -f, --format <format>  response format
+
+# example API call, sends JSON formatted response to stdout
+$ cbioportal-api-client getProfileData -s gbm_tcga_cnaseq -p gbm_tcga_mutations -g TP53
+```
+
 ---
 
 ## API Reference
-  
-* [cbioportal-api-client](#module_cbioportal-api-client)
-    * [module.exports(config)](#exp_module_cbioportal-api-client--module.exports) ⇒ <code>cbioPortal</code> ⏏
-        * _static_
-            * [.convertResponse(response)](#module_cbioportal-api-client--module.exports.convertResponse) ⇒ <code>Promise</code>
-        * _inner_
-            * [~cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal) : <code>Object</code>
-                * [.getTypesOfCancer()](#module_cbioportal-api-client--module.exports..cbioPortal+getTypesOfCancer) ⇒ <code>Promise</code>
-                * [.getCancerStudies()](#module_cbioportal-api-client--module.exports..cbioPortal+getCancerStudies) ⇒ <code>Promise</code>
-                * [.getGeneticProfiles(query)](#module_cbioportal-api-client--module.exports..cbioPortal+getGeneticProfiles) ⇒ <code>Promise(data)</code>
-                * [.getCaseLists(query)](#module_cbioportal-api-client--module.exports..cbioPortal+getCaseLists) ⇒ <code>Promise(data)</code>
-                * [.getProfileData()](#module_cbioportal-api-client--module.exports..cbioPortal+getProfileData) ⇒ <code>Promise(data)</code>
 
-<a name="exp_module_cbioportal-api-client--module.exports"></a>
-### module.exports(config) ⇒ <code>cbioPortal</code> ⏏
+## Modules
+
+<dl>
+<dt><a href="#module_cbioportal-api-client">cbioportal-api-client</a> ⇒ <code>cbioPortal</code></dt>
+<dd><p>Creates a new cBio Portal API client</p>
+</dd>
+<dt><a href="#module_cbioportal-api-client/utils/convertResponse">cbioportal-api-client/utils/convertResponse</a> ⇒ <code>Promise</code></dt>
+<dd><p>Converts tab delimited responses to JSON format</p>
+</dd>
+<dt><a href="#module_cbioportal-api-client/utils/summarizeAlterations">cbioportal-api-client/utils/summarizeAlterations</a></dt>
+<dd><p>Exports utility functions for summarizing gene alterations</p>
+</dd>
+</dl>
+
+<a name="module_cbioportal-api-client"></a>
+## cbioportal-api-client ⇒ <code>cbioPortal</code>
 Creates a new cBio Portal API client
 
-**Kind**: Exported function  
+**See**: [cbioPortal](#module_cbioportal-api-client..cbioPortal)  
 
@@ -46,47 +110,60 @@ | Param | Type | Description |
 ```
-<a name="module_cbioportal-api-client--module.exports.convertResponse"></a>
-#### module.exports.convertResponse(response) ⇒ <code>Promise</code>
-Converts tab delimited responses to JSON format
 
-**Kind**: static method of <code>[module.exports](#exp_module_cbioportal-api-client--module.exports)</code>  
-**Returns**: <code>Promise</code> - Resolves with the response JSON  
+* [cbioportal-api-client](#module_cbioportal-api-client) ⇒ <code>cbioPortal</code>
+    * [~cbioPortal](#module_cbioportal-api-client..cbioPortal) : <code>Object</code>
+        * [.getTypesOfCancer()](#module_cbioportal-api-client..cbioPortal+getTypesOfCancer) ⇒ <code>Promise</code>
+        * [.getCancerStudies()](#module_cbioportal-api-client..cbioPortal+getCancerStudies) ⇒ <code>Promise</code>
+        * [.getGeneticProfiles(query)](#module_cbioportal-api-client..cbioPortal+getGeneticProfiles) ⇒ <code>Promise</code>
+        * [.getCaseLists(query)](#module_cbioportal-api-client..cbioPortal+getCaseLists) ⇒ <code>Promise</code>
+        * [.getProfileData(query)](#module_cbioportal-api-client..cbioPortal+getProfileData) ⇒ <code>Promise</code>
 
-| Param | Type | Description |
-| --- | --- | --- |
-| response | <code>string</code> | TSV string |
 
-<a name="module_cbioportal-api-client--module.exports..cbioPortal"></a>
-#### module.exports~cbioPortal : <code>Object</code>
+-----
+
+<a name="module_cbioportal-api-client..cbioPortal"></a>
+### cbioportal-api-client~cbioPortal : <code>Object</code>
 cbioPortal API Object Prototype. Used as the object prototype
 when creating an API client object via the module factory method.
 
-**Kind**: inner constant of <code>[module.exports](#exp_module_cbioportal-api-client--module.exports)</code>  
-**See**: Use [CbioPortal()](module:cbioportal-api-client~CbioPortal) for object creation.  
+**Kind**: inner constant of <code>[cbioportal-api-client](#module_cbioportal-api-client)</code>  
+**See**: Use [CbioPortal()](#module_cbioportal-api-client) for object creation.  
 
-* [~cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal) : <code>Object</code>
-    * [.getTypesOfCancer()](#module_cbioportal-api-client--module.exports..cbioPortal+getTypesOfCancer) ⇒ <code>Promise</code>
-    * [.getCancerStudies()](#module_cbioportal-api-client--module.exports..cbioPortal+getCancerStudies) ⇒ <code>Promise</code>
-    * [.getGeneticProfiles(query)](#module_cbioportal-api-client--module.exports..cbioPortal+getGeneticProfiles) ⇒ <code>Promise(data)</code>
-    * [.getCaseLists(query)](#module_cbioportal-api-client--module.exports..cbioPortal+getCaseLists) ⇒ <code>Promise(data)</code>
-    * [.getProfileData()](#module_cbioportal-api-client--module.exports..cbioPortal+getProfileData) ⇒ <code>Promise(data)</code>
+* [~cbioPortal](#module_cbioportal-api-client..cbioPortal) : <code>Object</code>
+    * [.getTypesOfCancer()](#module_cbioportal-api-client..cbioPortal+getTypesOfCancer) ⇒ <code>Promise</code>
+    * [.getCancerStudies()](#module_cbioportal-api-client..cbioPortal+getCancerStudies) ⇒ <code>Promise</code>
+    * [.getGeneticProfiles(query)](#module_cbioportal-api-client..cbioPortal+getGeneticProfiles) ⇒ <code>Promise</code>
+    * [.getCaseLists(query)](#module_cbioportal-api-client..cbioPortal+getCaseLists) ⇒ <code>Promise</code>
+    * [.getProfileData(query)](#module_cbioportal-api-client..cbioPortal+getProfileData) ⇒ <code>Promise</code>
 
-<a name="module_cbioportal-api-client--module.exports..cbioPortal+getTypesOfCancer"></a>
-##### cbioPortal.getTypesOfCancer() ⇒ <code>Promise</code>
+
+-----
+
+<a name="module_cbioportal-api-client..cbioPortal+getTypesOfCancer"></a>
+#### cbioPortal.getTypesOfCancer() ⇒ <code>Promise</code>
 Retrieves a list of all the clinical types of cancer stored on the server.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - resolves with JSON data  
-<a name="module_cbioportal-api-client--module.exports..cbioPortal+getCancerStudies"></a>
-##### cbioPortal.getCancerStudies() ⇒ <code>Promise</code>
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
+**Returns**: <code>Promise</code> - See fullfills/rejects  
+**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+
+-----
+
+<a name="module_cbioportal-api-client..cbioPortal+getCancerStudies"></a>
+#### cbioPortal.getCancerStudies() ⇒ <code>Promise</code>
 Retrieves meta-data regarding cancer studies stored on the server.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - resolves with JSON data  
-<a name="module_cbioportal-api-client--module.exports..cbioPortal+getGeneticProfiles"></a>
-##### cbioPortal.getGeneticProfiles(query) ⇒ <code>Promise(data)</code>
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
+**Returns**: <code>Promise</code> - See fullfills/rejects  
+**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+
+-----
+
+<a name="module_cbioportal-api-client..cbioPortal+getGeneticProfiles"></a>
+#### cbioPortal.getGeneticProfiles(query) ⇒ <code>Promise</code>
 Retrieves meta-data regarding all genetic profiles, e.g.
 mutation or copy number profiles, stored about a specific cancer study.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal)</code>  
-**Returns**: <code>Promise(data)</code> - resolves with JSON data  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
+**Returns**: <code>Promise</code> - See fullfills/rejects  
+**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
 
@@ -98,4 +175,7 @@ | Param | Type | Description |
 
-<a name="module_cbioportal-api-client--module.exports..cbioPortal+getCaseLists"></a>
-##### cbioPortal.getCaseLists(query) ⇒ <code>Promise(data)</code>
+
+-----
+
+<a name="module_cbioportal-api-client..cbioPortal+getCaseLists"></a>
+#### cbioPortal.getCaseLists(query) ⇒ <code>Promise</code>
 Retrieves meta-data regarding all case lists stored about a specific cancer study.
@@ -107,3 +187,4 @@
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal)</code>  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
+**Fulfill**: JSON formatted response  
 
@@ -115,10 +196,15 @@ | Param | Type | Description |
 
-<a name="module_cbioportal-api-client--module.exports..cbioPortal+getProfileData"></a>
-##### cbioPortal.getProfileData() ⇒ <code>Promise(data)</code>
+
+-----
+
+<a name="module_cbioportal-api-client..cbioPortal+getProfileData"></a>
+#### cbioPortal.getProfileData(query) ⇒ <code>Promise</code>
 Retrieves genomic profile data for one or more genes.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client--module.exports..cbioPortal)</code>  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
+**Fulfill**: JSON formatted response  
 
 | Param | Type | Description |
 | --- | --- | --- |
+| query | <code>Object</code> |  |
 | options.case_set_id | <code>string</code> | A unique ID used to identify the case list ID in subsequent interface calls. This is a human readable ID. For example, "gbm_all" identifies all cases profiles in the TCGA GBM study. |
@@ -128,1 +214,72 @@ | options.genetic_profile_id | <code>Array.&lt;string&gt;</code> &#124; <code>string</code> | One or more genetic profile IDs |
 
+
+-----
+
+<a name="module_cbioportal-api-client/utils/convertResponse"></a>
+## cbioportal-api-client/utils/convertResponse ⇒ <code>Promise</code>
+Converts tab delimited responses to JSON format
+
+**Returns**: <code>Promise</code> - Resolves with the response JSON  
+
+| Param | Type | Description |
+| --- | --- | --- |
+| response | <code>string</code> | TSV string |
+
+
+-----
+
+<a name="module_cbioportal-api-client/utils/summarizeAlterations"></a>
+## cbioportal-api-client/utils/summarizeAlterations
+Exports utility functions for summarizing gene alterations
+
+
+* [cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)
+    * [.summarizeMutations(mutations)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeMutations) ⇒ <code>Array</code>
+    * [.summarizeCopyNumberAlterations(copyNumberAlterations)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations) ⇒ <code>Array</code>
+    * [.summarizeAlterations(response)](#module_cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations) ⇒ <code>Promise</code>
+
+
+-----
+
+<a name="module_cbioportal-api-client/utils/summarizeAlterations.summarizeMutations"></a>
+### cbioportal-api-client/utils/summarizeAlterations.summarizeMutations(mutations) ⇒ <code>Array</code>
+Summarize mutations
+
+**Kind**: static method of <code>[cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)</code>  
+**Returns**: <code>Array</code> - Array of summaries  
+
+| Param | Type | Description |
+| --- | --- | --- |
+| mutations | <code>Array</code> | Array of mutation rows as parsed by this library |
+
+
+-----
+
+<a name="module_cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations"></a>
+### cbioportal-api-client/utils/summarizeAlterations.summarizeCopyNumberAlterations(copyNumberAlterations) ⇒ <code>Array</code>
+Summarize copy number alterations
+
+**Kind**: static method of <code>[cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)</code>  
+**Returns**: <code>Array</code> - Array of summaries  
+
+| Param | Type | Description |
+| --- | --- | --- |
+| copyNumberAlterations | <code>Array</code> | Array of copy number alteration rows as parsed by this library |
+
+
+-----
+
+<a name="module_cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations"></a>
+### cbioportal-api-client/utils/summarizeAlterations.summarizeAlterations(response) ⇒ <code>Promise</code>
+Converts tab delimited responses to JSON format
+
+**Kind**: static method of <code>[cbioportal-api-client/utils/summarizeAlterations](#module_cbioportal-api-client/utils/summarizeAlterations)</code>  
+**Returns**: <code>Promise</code> - Resolves with the response JSON  
+
+| Param | Type | Description |
+| --- | --- | --- |
+| response | <code>string</code> | TSV string |
+
+
+-----
+

test/index.js

 require('app-module-path').addPath(__dirname + './../');
 require('./lib');
+require('./utils/summarizeAlterations');

test/lib.js

@@ -63,1 +63,15 @@ import Test from 'blue-tape';
 });
+
+Test('cbioPortal.getProfileData()', t => {
+  Nock('http://www.cbioportal.org')
+    .get('/webservice.do')
+    .query({ cmd: 'getProfileData', case_set_id: 'gbm_tcga_cnaseq' })
+    .replyWithFile(200, __dirname + '/responses/getProfileData.tsv');
+
+  return cbioPortal.getProfileData({ case_set_id: 'gbm_tcga_cnaseq' })
+    .then(response => {
+      t.ok(Array.isArray(response), 'should return an array');
+      t.ok(response[0].GENE_ID, 'should return profile data');
+      t.equals(response.length, 1, 'should have a single row');
+    });
+});

New alerts

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

180494

increased by41.21%

Number of package files

33

increased by94.12%

Lines of code

833

increased by126.36%

Number of lines in readme file

281

increased by126.61%

Worsened metrics

Dependency count

10

increased by25%

Dev dependency count

16

increased by6.67%

Number of low supply chain risk alerts

1

increased byInfinity%

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• + Addedcommander@^2.9.0

• + Addedlodash@^4.0.0

• + Addedcommander@2.20.3(transitive)