made convertResponse browser compatible

nathanmarks · Jan 28, 2016 · c669c50 · c669c50
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![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)
 [![Dependency Status](https://david-dm.org/nathanmarks/cbioportal-api-client.svg?style=flat-square)](https://david-dm.org/nathanmarks/cbioportal-api-client)
 
-[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) (***soon:** just finalizing the browser build).
+[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) (**soon:** just finalizing the browser build).
 
 This library can be used programatically or via the command line.
 
@@ -82,9 +82,8 @@ $ cbioportal-api-client getAlterationSummary -s gbm_tcga_cnaseq -p gbm_tcga_muta
 ## 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">cbioportal-api-client</a></dt>
+<dd></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>
@@ -94,17 +93,35 @@ $ cbioportal-api-client getAlterationSummary -s gbm_tcga_cnaseq -p gbm_tcga_muta
 </dl>
 
 <a name="module_cbioportal-api-client"></a>
-## cbioportal-api-client ⇒ <code>cbioPortal</code>
+## cbioportal-api-client
+
+* [cbioportal-api-client](#module_cbioportal-api-client)
+    * _exports_
+        * [⏏ exports.default(config)](#exp_module_cbioportal-api-client.default) ⇒ <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+    * _inner_
+        * [~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="exp_module_cbioportal-api-client.default"></a>
+### cbioportal-api-client ⏏ exports.default(config) ⇒ <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
 Creates a new cBio Portal API client
 
-**See**: [cbioPortal](#module_cbioportal-api-client..cbioPortal)  
+**Kind**: exports method of <code>[cbioportal-api-client](#module_cbioportal-api-client)</code>
+**Returns**: <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
 
 | Param | Type | Description |
 | --- | --- | --- |
 | config | <code>Object</code> | Configuration options object. |
 | config.requestOpts | <code>Object</code> | Override the request congfiguration object. |
 
-**Example**  
+**Example**
 Basic usage:
 
 ```javascript
@@ -118,24 +135,15 @@ cbioPortal.getCancerStudies()
   });
 ```
 
-* [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>
-
-
 -----
 
 <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>[cbioportal-api-client](#module_cbioportal-api-client)</code>  
-**See**: Use [CbioPortal()](#module_cbioportal-api-client) 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..cbioPortal) : <code>Object</code>
     * [.getTypesOfCancer()](#module_cbioportal-api-client..cbioPortal+getTypesOfCancer) ⇒ <code>Promise</code>
@@ -151,19 +159,19 @@ when creating an API client object via the module factory method.
 #### 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..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - See fullfills/rejects  
-**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+**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..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - See fullfills/rejects  
-**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+**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
 
 -----
 
@@ -172,9 +180,9 @@ Retrieves meta-data regarding cancer studies stored on the server.
 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..cbioPortal)</code>  
-**Returns**: <code>Promise</code> - See fullfills/rejects  
-**Fulfills**: <code>Array</code> response data converted from TSV to JSON  
+**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
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -192,8 +200,9 @@ For example, a within a particular study, only some cases may have sequence data
 
 Multiple case lists may be associated with each cancer study, and this method enables you to retrieve meta-data regarding all of these case lists.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Fulfill**: JSON formatted response  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Returns**: <code>Promise</code>
+**Fulfill**: JSON formatted response
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -209,8 +218,9 @@ Retrieves genomic profile data for one or more genes.
 
 **Note:** If you pass in multiple genetic profile IDs and multiple genes, the library will make multiple requests as the API does not support this type of query.
 
-**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>  
-**Fulfill**: JSON formatted response  
+**Kind**: instance method of <code>[cbioPortal](#module_cbioportal-api-client..cbioPortal)</code>
+**Returns**: <code>Promise</code>
+**Fulfill**: JSON formatted response
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -226,7 +236,7 @@ Retrieves genomic profile data for one or more genes.
 ## cbioportal-api-client/utils/convertResponse ⇒ <code>Promise</code>
 Converts tab delimited responses to JSON format
 
-**Returns**: <code>Promise</code> - Resolves with the response JSON  
+**Returns**: <code>Promise</code> - Resolves with the response JSON
 
 | Param | Type | Description |
 | --- | --- | --- |
@@ -239,14 +249,14 @@ Converts tab delimited responses to JSON format
 ## cbioportal-api-client/utils/summarizeAlterations ⇒ <code>Promise</code>
 Summarizes alterations for results
 
-**Returns**: <code>Promise</code> - Resolves with the summary  
-**Fulfills**: <code>Object</code> Object with results, see example  
+**Returns**: <code>Promise</code> - Resolves with the summary
+**Fulfills**: <code>Object</code> Object with results, see example
 
 | Param | Type | Description |
 | --- | --- | --- |
 | dataSets | <code>Object</code> &#124; <code>Array</code> | Converted response dataset(s) |
 
-**Example**  
+**Example**
 Basic Usage:
 
 ```javascript

diff --git a/docs/partials/.DS_Store b/docs/partials/.DS_Store
diff --git a/docs/partials/shared/signature/sig-link-html.hbs b/docs/partials/shared/signature/sig-link-html.hbs
@@ -0,0 +1,14 @@
+{{#if name}}{{#sig no-gfm=true ~}}
+{{{@depOpen}~}}
+<a href="#{{{anchorName}}}">
+{{~{@codeOpen}~}}
+{{#if @prefix}}{{@prefix}} {{/if~}}
+{{@accessSymbol}}{{#if (isEvent)}}"{{{name}}}"{{else}}{{{name}}}{{/if~}}
+{{~#if @methodSign}}{{#if (isEvent)}} {{@methodSign}}{{else}}{{@methodSign}}{{/if}}{{/if~}}
+{{{@codeClose}~}}
+</a>
+{{~#if @returnSymbol}} {{@returnSymbol}}{{/if~}}
+{{#if @returnTypes}} {{>linked-type-list types=@returnTypes html=true delimiter=" | " }}{{/if~}}
+{{#if @suffix}} {{@suffix}}{{/if~}}
+{{{@depClose}~}}
+{{~/sig}}{{/if~}}
diff --git a/docs/partials/shared/signature/sig-link-parent.hbs b/docs/partials/shared/signature/sig-link-parent.hbs
@@ -0,0 +1,13 @@
+{{#if name}}{{#sig~}}
+{{{@depOpen}~}}
+[{{{@codeOpen}~}}
+{{#if @prefix}}{{@prefix}} {{/if~}}
+{{#if (isClassMember)}}{{@parent~}}{{/if~}}
+{{@accessSymbol}}{{#if (isEvent)}}"{{{name}}}"{{else}}{{{name}}}{{/if~}}
+{{~#if @methodSign}}{{#if (isEvent)}} {{@methodSign}}{{else}}{{@methodSign}}{{/if}}{{/if~}}
+{{{@codeClose}}}](#{{{anchorName}}})
+{{~#if @returnSymbol}} {{@returnSymbol}}{{/if~}}
+{{#if @returnTypes}} {{>linked-type-list types=@returnTypes delimiter=" &#124; " }}{{/if~}}
+{{#if @suffix}} {{@suffix}}{{/if~}}
+{{{@depClose}~}}
+{{~/sig}}{{/if~}}
diff --git a/docs/partials/shared/signature/sig-link.hbs b/docs/partials/shared/signature/sig-link.hbs
@@ -0,0 +1,14 @@
+{{#if virtual}}*{{/if}}{{#with (parentObject)}}{{#if virtual}}*{{/if~}}{{/with~}}
+{{#if name}}{{#sig~}}
+{{{@depOpen}~}}
+[{{{@codeOpen}~}}
+{{#if @prefix}}{{@prefix}} {{/if~}}
+{{#if @suffix}}{{@suffix}} {{/if~}}
+{{@accessSymbol}}{{#if (isEvent)}}"{{{name}}}"{{else}}{{{name}}}{{/if~}}
+{{~#if @methodSign}}{{#if (isEvent)}} {{@methodSign}}{{else}}{{@methodSign}}{{/if}}{{/if~}}
+{{{@codeClose}}}](#{{{anchorName}}})
+{{~#if @returnSymbol}} {{@returnSymbol}}{{/if~}}
+{{#if @returnTypes}} {{>linked-type-list types=@returnTypes delimiter=" &#124; " }}{{/if~}}
+{{{@depClose}~}}
+{{~/sig}}{{/if~}}
+{{#if virtual}}*{{/if}}{{#with (parentObject)}}{{#if virtual}}*{{/if~}}{{/with~}}
diff --git a/docs/partials/shared/signature/sig-name.hbs b/docs/partials/shared/signature/sig-name.hbs
@@ -0,0 +1,15 @@
+{{#if virtual}}*{{/if}}{{#with (parentObject)}}{{#if virtual}}*{{/if~}}{{/with~}}
+{{#if name}}{{#sig~}}
+{{{@depOpen}~}}
+{{{@codeOpen}~}}
+{{#if @prefix}}{{@prefix}} {{/if~}}
+{{@parent~}}
+{{#if @suffix}} {{@suffix}} {{/if~}}
+{{@accessSymbol}}{{#if (isEvent)}}"{{{name}}}"{{else}}{{{name}}}{{/if~}}
+{{#if @methodSign}}{{#if (isEvent)}} {{@methodSign}}{{else}}{{@methodSign}}{{/if}}{{/if~}}
+{{{@codeClose}~}}
+{{#if @returnSymbol}} {{@returnSymbol}}{{/if~}}
+{{#if @returnTypes}} {{>linked-type-list types=@returnTypes delimiter=" &#124; " }}{{/if~}}
+{{{@depClose}~}}
+{{~/sig}}{{/if~}}
+{{#if virtual}}*{{/if}}{{#with (parentObject)}}{{#if virtual}}*{{/if~}}{{/with~}}
diff --git a/lib/index.js b/lib/index.js
@@ -14,6 +14,43 @@ import {
   summarizeAlterations
 } from './utils';
 
+/**
+ * @module cbioportal-api-client
+ */
+
+/**
+ * Creates a new cBio Portal API client
+ *
+ * @example
+ *
+ * Basic usage:
+ *
+ * ```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
+ *   });
+ * ```
+ *
+ * @param {Object} config Configuration options object.
+ * @param {Object} config.requestOpts Override the request congfiguration object.
+ * @returns {module:cbioportal-api-client~cbioPortal}
+ */
+export default function CbioPortal ({ requestOpts = false } = {}) {
+  return Object.assign(Object.create(cbioPortal), {
+    requestOpts: _defaults(requestOpts, {
+      headers: {
+        'User-Agent': 'cbioportal-api-client.js/0.0.1'
+      },
+      uri: 'http://www.cbioportal.org/webservice.do'
+    })
+  });
+}
+
 /**
  * parseArray
  *
@@ -29,8 +66,6 @@ function parseArray (x) {
  * cbioPortal API Object Prototype. Used as the object prototype
  * when creating an API client object via the module factory method.
  *
- * @memberOf module:cbioportal-api-client
- * @alias module:cbioportal-api-client~cbioPortal
  * @see Use {@link module:cbioportal-api-client|CbioPortal()} for object creation.
  * @type {Object}
  */
@@ -147,40 +182,3 @@ const cbioPortal = {
   }
 
 };
-
-/**
- * Creates a new cBio Portal API client
- *
- * @example
- *
- * Basic usage:
- *
- * ```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
- *   });
- * ```
- *
- * @module cbioportal-api-client
- * @see {@link module:cbioportal-api-client~cbioPortal|cbioPortal}
- * @param {Object} config Configuration options object.
- * @param {Object} config.requestOpts Override the request congfiguration object.
- * @returns {cbioPortal}
- */
-function CbioPortal ({ requestOpts = false } = {}) {
-  return Object.assign(Object.create(cbioPortal), {
-    requestOpts: _defaults(requestOpts, {
-      headers: {
-        'User-Agent': 'cbioportal-api-client.js/0.0.1'
-      },
-      uri: 'http://www.cbioportal.org/webservice.do'
-    })
-  });
-}
-
-export default CbioPortal;
diff --git a/lib/utils/convertResponse.js b/lib/utils/convertResponse.js
@@ -2,7 +2,9 @@ import Promise from 'bluebird';
 import CsvParser from 'csv-parser';
 import _map from 'lodash/map';
 import _transform from 'lodash/transform';
-import { Readable } from 'stream';
+import { canUseDom } from 'fbjs/lib/ExecutionEnvironment';
+
+const Readable = canUseDom ? require('stream-browserify').Readable : require('stream').Readable;
 
 const copyNumberRegexp = /^.*#.*(?:COPY_NUMBER_ALTERATION)\n/mg;
 const mutationRegexp = /^.*#.*(?:MUTATION_EXTENDED)\n/mg;

diff --git a/package.json b/package.json
@@ -7,8 +7,8 @@
     "cbioportal-api-client": "./bin/cbioportal-api-client"
   },
   "scripts": {
-    "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\"",
+    "build": "npm run clean:dist && babel lib -d dist",
+    "build:dev": "nodemon -w lib --exec \"npm run clean:dist && babel lib -d dist\"",
     "clean": "npm run clean:dist && npm run clean:coverage",
     "clean:dist": "rimraf dist",
     "clean:coverage": "rimraf coverage",
@@ -62,8 +62,10 @@
     "commander": "^2.9.0",
     "continuation-local-storage": "^3.1.4",
     "csv-parser": "^1.9.2",
+    "fbjs": "^0.7.0",
     "in-publish": "^2.0.0",
     "lodash": "^4.0.0",
-    "request-promise": "^2.0.0"
+    "request-promise": "^2.0.0",
+    "stream-browserify": "^2.0.1"
   }
 }