cbioportal-api-client - npm Package Compare versions

Comparing version 0.2.13 to 0.3.0

dist/index.js

@@ -7,2 +7,6 @@ 'use strict';
 
+var _keys = require('babel-runtime/core-js/object/keys');
+
+var _keys2 = _interopRequireDefault(_keys);
+
 var _create = require('babel-runtime/core-js/object/create');
@@ -21,5 +25,5 @@
 
-var _requestPromise = require('request-promise');
+var _isomorphicFetch = require('isomorphic-fetch');
 
-var _requestPromise2 = _interopRequireDefault(_requestPromise);
+var _isomorphicFetch2 = _interopRequireDefault(_isomorphicFetch);
 
@@ -80,5 +84,4 @@ var _reduce2 = require('lodash/reduce');
       headers: {
-        'User-Agent': 'cbioportal-api-client.js/0.0.1'
-      },
-      uri: 'http://www.cbioportal.org/webservice.do'
+        'User-Agent': 'cbioportal-api-client.js/1.0.0'
+      }
     })
@@ -122,9 +125,11 @@ });
     var cmd = 'get' + endpoint;
+    var qsObj = (0, _assign2.default)((0, _utils.formatQuery)(query), { cmd: cmd });
+    var qs = (0, _keys2.default)(qsObj).reverse().map(function (key) {
+      return key + '=' + encodeURIComponent(qsObj[key]);
+    }).join('&');
 
-    var requestOpts = (0, _assign2.default)({
-      qs: (0, _assign2.default)((0, _utils.formatQuery)(query), { cmd: cmd })
-    }, this.requestOpts);
-
-    return (0, _requestPromise2.default)(requestOpts).then(function (response) {
-      return (0, _utils.convertResponse)(response, cmd);
+    return (0, _isomorphicFetch2.default)('http://www.cbioportal.org/webservice.do?' + qs, this.requestOpts).then(function (response) {
+      return response.text();
+    }).then(function (responseText) {
+      return (0, _utils.convertResponse)(responseText, cmd);
     });
@@ -131,0 +136,0 @@ },

dist/utils/convertResponse.js

@@ -11,2 +11,6 @@ 'use strict';
 
+var _promise = require('babel-runtime/core-js/promise');
+
+var _promise2 = _interopRequireDefault(_promise);
+
 Object.defineProperty(exports, "__esModule", {
@@ -17,6 +21,2 @@ value: true
 
-var _bluebird = require('bluebird');
-
-var _bluebird2 = _interopRequireDefault(_bluebird);
-
 var _csvParser = require('csv-parser');
@@ -34,8 +34,6 @@
 
-var _ExecutionEnvironment = require('fbjs/lib/ExecutionEnvironment');
+var _stream = require('stream');
 
 function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; }
 
-var Readable = _ExecutionEnvironment.canUseDom ? require('stream-browserify').Readable : require('stream').Readable;
-
 var copyNumberRegexp = /^.*#.*(?:COPY_NUMBER_ALTERATION)\n/mg;
@@ -60,4 +58,4 @@ var mutationRegexp = /^.*#.*(?:MUTATION_EXTENDED)\n/mg;
 
-  return new _bluebird2.default(function (resolve) {
-    var stream = new Readable();
+  return new _promise2.default(function (resolve) {
+    var stream = new _stream.Readable();
     var rows = [];
@@ -64,0 +62,0 @@ stream._read = function () {}; // eslint-disable-line no-underscore-dangle

dist/utils/summarizeAlterations.js

 'use strict';
 
+var _promise = require('babel-runtime/core-js/promise');
+
+var _promise2 = _interopRequireDefault(_promise);
+
 var _typeof2 = require('babel-runtime/helpers/typeof');
@@ -16,6 +20,2 @@
 
-var _bluebird = require('bluebird');
-
-var _bluebird2 = _interopRequireDefault(_bluebird);
-
 var _map2 = require('lodash/map');
@@ -54,2 +54,4 @@
  */
+/* eslint-disable no-param-reassign  */
+
 function reduceCaseIds(key) {
@@ -71,4 +73,2 @@ return function (cases, n) {
  */
-/* eslint-disable no-param-reassign  */
-
 function summarizer(cases, alterationFilter) {
@@ -193,3 +193,3 @@ var summary = (0, _transform3.default)(cases, function (result, n, key) {
 
-  return new _bluebird2.default(function (resolve) {
+  return new _promise2.default(function (resolve) {
 
@@ -196,0 +196,0 @@ var rows = (0, _flatten3.default)((0, _map3.default)((0, _flattenDeep3.default)(dataSets), function (set) {

lib/index.js

@@ -8,3 +8,3 @@ /**
 
-import Request from 'request-promise';
+import Fetch from 'isomorphic-fetch';
 import _reduce from 'lodash/reduce';
@@ -48,5 +48,4 @@ import _defaults from 'lodash/defaults';
       headers: {
-        'User-Agent': 'cbioportal-api-client.js/0.0.1'
-      },
-      uri: 'http://www.cbioportal.org/webservice.do'
+        'User-Agent': 'cbioportal-api-client.js/1.0.0'
+      }
     })
@@ -87,9 +86,10 @@ });
     const cmd = `get${endpoint}`;
+    const qsObj = Object.assign(formatQuery(query), { cmd });
+    const qs = Object.keys(qsObj).reverse().map(key => {
+      return key + '=' + encodeURIComponent(qsObj[key]);
+    }).join('&');
 
-    const requestOpts = Object.assign({
-      qs: Object.assign(formatQuery(query), { cmd })
-    }, this.requestOpts);
-
-    return Request(requestOpts)
-      .then(response => convertResponse(response, cmd));
+    return Fetch(`http://www.cbioportal.org/webservice.do?${qs}`, this.requestOpts)
+      .then(response => response.text())
+      .then(responseText => convertResponse(responseText, cmd));
   },
@@ -96,0 +96,0 @@

lib/utils/convertResponse.js

@@ -1,9 +0,6 @@
-import Promise from 'bluebird';
 import CsvParser from 'csv-parser';
 import _map from 'lodash/map';
 import _transform from 'lodash/transform';
-import { canUseDom } from 'fbjs/lib/ExecutionEnvironment';
+import { Readable } from 'stream';
 
-const Readable = canUseDom ? require('stream-browserify').Readable : require('stream').Readable;
-
 const copyNumberRegexp = /^.*#.*(?:COPY_NUMBER_ALTERATION)\n/mg;
@@ -10,0 +7,0 @@ const mutationRegexp = /^.*#.*(?:MUTATION_EXTENDED)\n/mg;

lib/utils/summarizeAlterations.js

 /* eslint-disable no-param-reassign  */
 
-import Promise from 'bluebird';
 import _map from 'lodash/map';
@@ -5,0 +4,0 @@ import _uniq from 'lodash/uniq';

package.json

 {
   "name": "cbioportal-api-client",
-  "version": "0.2.13",
+  "version": "0.3.0",
   "description": "cBio Portal API client with promises and response parsing",
@@ -10,3 +10,5 @@ "main": "dist/index.js",
   "scripts": {
-    "build": "npm run clean:dist && babel lib -d dist",
+    "build": "npm run clean:dist && babel lib -d dist && npm run build:webpack",
+    "build:webpack": "cross-env NODE_ENV=production webpack --config webpack.config.prod.js",
+    "build:webpack:stats": "cross-env NODE_ENV=production webpack --config webpack.config.prod.js --profile --json > stats.json",
     "build:dev": "nodemon -w lib --exec \"npm run clean:dist && babel lib -d dist\"",
@@ -41,2 +43,3 @@ "clean": "npm run clean:dist && npm run clean:coverage",
     "babel-eslint": "^5.0.0-beta6",
+    "babel-loader": "^6.2.1",
     "babel-plugin-transform-es2015-modules-commonjs": "^6.4.5",
@@ -48,3 +51,5 @@ "babel-plugin-transform-runtime": "^6.4.0",
     "blue-tape": "^0.1.11",
+    "bluebird": "^3.1.5",
     "coveralls": "^2.11.6",
+    "cross-env": "^1.0.7",
     "ddata": "github:nathanmarks/ddata#personal-modifications",
@@ -56,2 +61,3 @@ "eslint": "^1.10.3",
     "jsdoc-to-markdown": "^1.3.3",
+    "json-loader": "^0.5.4",
     "nock": "^5.2.1",
@@ -61,16 +67,13 @@ "rimraf": "^2.5.0",
     "tap-xunit": "^1.3.1",
-    "tape": "^4.4.0"
+    "tape": "^4.4.0",
+    "webpack": "^1.12.12"
   },
   "dependencies": {
-    "bluebird": "^3.1.1",
-    "cls-bluebird": "^1.0.1",
     "commander": "^2.9.0",
-    "continuation-local-storage": "^3.1.4",
     "csv-parser": "^1.9.2",
-    "fbjs": "^0.7.0",
     "in-publish": "^2.0.0",
+    "isomorphic-fetch": "^2.2.1",
     "lodash": "^4.0.0",
-    "request-promise": "^2.0.0",
-    "stream-browserify": "^2.0.1"
+    "readable-stream": "^2.0.5"
   }
 }

README.md

@@ -6,3 +6,3 @@ # cBio Portal 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).
 
@@ -9,0 +9,0 @@ This library can be used programatically or via the command line.

No alert changes

Improved metrics

Total package byte prevSize

331835

increased by0.33%

Dependency count

6

decreased by-40%

Number of package files

58

increased by1.75%

Lines of code

1698

increased by2.6%

Worsened metrics

Dev dependency count

26

increased by23.81%

Dependency changes

• + Addedisomorphic-fetch@^2.2.1

• + Addedreadable-stream@^2.0.5

• - Removedbluebird@^3.1.1

• - Removedcls-bluebird@^1.0.1

• - Removedcontinuation-local-storage@^3.1.4

• - Removedfbjs@^0.7.0

• - Removedrequest-promise@^2.0.0

• - Removedstream-browserify@^2.0.1

• - Removedajv@6.12.6(transitive)

• - Removedasap@2.0.6(transitive)

• - Removedasn1@0.2.6(transitive)

• - Removedassert-plus@1.0.0(transitive)

• - Removedasync-listener@0.6.10(transitive)

• - Removedasynckit@0.4.0(transitive)

• - Removedaws-sign2@0.7.0(transitive)

• - Removedaws4@1.13.2(transitive)

• - Removedbcrypt-pbkdf@1.0.2(transitive)

• - Removedbluebird@2.11.03.7.2(transitive)

• - Removedcaseless@0.12.0(transitive)

• - Removedcls-bluebird@1.1.3(transitive)

• - Removedcombined-stream@1.0.8(transitive)

• - Removedcontinuation-local-storage@3.2.1(transitive)

• - Removedcore-js@1.2.7(transitive)

• - Removedcore-util-is@1.0.2(transitive)

• - Removeddashdash@1.14.1(transitive)

• - Removeddelayed-stream@1.0.0(transitive)

• - Removedecc-jsbn@0.1.2(transitive)

• - Removedemitter-listener@1.1.2(transitive)

• - Removedextend@3.0.2(transitive)

• - Removedextsprintf@1.3.0(transitive)

• - Removedfast-deep-equal@3.1.3(transitive)

• - Removedfast-json-stable-stringify@2.1.0(transitive)

• - Removedfbjs@0.7.2(transitive)

• - Removedforever-agent@0.6.1(transitive)

• - Removedform-data@2.3.3(transitive)

• - Removedgetpass@0.1.7(transitive)

• - Removedhar-schema@2.0.0(transitive)

• - Removedhar-validator@5.1.5(transitive)

• - Removedhttp-signature@1.2.0(transitive)

• - Removedis-bluebird@1.0.2(transitive)

• - Removedis-typedarray@1.0.0(transitive)

• - Removedisstream@0.1.2(transitive)

• - Removedjs-tokens@4.0.0(transitive)

• - Removedjsbn@0.1.1(transitive)

• - Removedjson-schema@0.4.0(transitive)

• - Removedjson-schema-traverse@0.4.1(transitive)

• - Removedjsprim@1.4.2(transitive)

• - Removedloose-envify@1.4.0(transitive)

• - Removedmime-db@1.52.0(transitive)

• - Removedmime-types@2.1.35(transitive)

• - Removedoauth-sign@0.9.0(transitive)

• - Removedperformance-now@2.1.0(transitive)

• - Removedpromise@7.3.1(transitive)

• - Removedpsl@1.15.0(transitive)

• - Removedpunycode@2.3.1(transitive)

• - Removedqs@6.5.3(transitive)

• - Removedrequest@2.88.2(transitive)

• - Removedrequest-promise@2.0.1(transitive)

• - Removedsafe-buffer@5.2.1(transitive)

• - Removedsemver@5.7.2(transitive)

• - Removedshimmer@1.2.1(transitive)

• - Removedsshpk@1.18.0(transitive)

• - Removedstream-browserify@2.0.2(transitive)

• - Removedtough-cookie@2.5.0(transitive)

• - Removedtunnel-agent@0.6.0(transitive)

• - Removedtweetnacl@0.14.5(transitive)

• - Removedua-parser-js@0.7.40(transitive)

• - Removeduri-js@4.4.1(transitive)

• - Removeduuid@3.4.0(transitive)

• - Removedverror@1.10.0(transitive)