Migrate oncoprintjs

package.json

@@ -83,11 +83,10 @@
     "@babel/plugin-transform-modules-commonjs": "^7.4.4",
     "@babel/preset-env": "^7.4.4",
     "@babel/preset-react": "^7.0.0",
-    "@rollup/plugin-commonjs": "^11.0.0",
-    "@rollup/plugin-json": "^4.0.2",
-    "@rollup/plugin-node-resolve": "^6.0.0",
-    "@rollup/plugin-url": "^4.0.0",
-    "@svgr/rollup": "^4.2.0",
+    "@rollup/plugin-commonjs": "^22.0.0",
+    "@rollup/plugin-json": "^4.1.0",
+    "@rollup/plugin-node-resolve": "^13.3.0",
+    "@rollup/plugin-image": "^2.1.1",
     "@types/chai": "3.5.2",
     "@types/chai-enzyme": "^0.6.2",
     "@types/chart.js": "^2.4.6",
@@ -220,7 +219,7 @@
     "object-sizeof": "^1.2.0",
     "oncokb-styles": "~1.3.0",
     "oncokb-ts-api-client": "^1.3.0",
-    "oncoprintjs": "5.0.4",
+    "oncoprintjs": "^6.0.0-beta.0",
     "pako": "2.0.2",
     "parameter-validator": "^1.0.2",
     "path-browserify": "^1.0.1",
@@ -293,11 +292,12 @@
     "reselect": "^2.5.4",
     "resolve-url-loader": "^1.6.1",
     "responsive-fixed-data-table": "^2.0.0",
-    "rollup": "^1.32.1",
-    "rollup-plugin-auto-external": "^2.0.0",
-    "rollup-plugin-postcss": "^2.0.3",
-    "rollup-plugin-sourcemaps": "^0.4.2",
-    "rollup-plugin-typescript2": "^0.27.0",
+    "rollup": "^2.73.0",
+    "rollup-plugin-node-externals": "^4.0.0",
+    "rollup-plugin-postcss": "^2.9.0",
+    "rollup-plugin-sourcemaps": "^0.6.3",
+    "rollup-plugin-typescript2": "^0.31.2",
+    "rollup-plugin-web-worker-loader": "^1.6.1",
     "route-parser": "0.0.5",
     "sass": "^1.32.4",
     "sass-loader": "10.1.1",

packages/cbioportal-clinical-timeline/package.json

@@ -40,7 +40,7 @@
   "dependencies": {
     "autobind-decorator": "^2.1.0",
     "cbioportal-frontend-commons": "^0.5.23",
-    "lodash": "^4.17.11",
+    "lodash": "^4.17.15",
     "react-bootstrap": "^0.31.5",
     "react-overlays": "0.7.4",
     "typescript": "4.0.3"

packages/cbioportal-frontend-commons/package.json

@@ -41,7 +41,7 @@
     "cbioportal-utils": "^0.3.16",
     "classnames": "^2.2.5",
     "jquery": "^3.2.1",
-    "lodash": "^4.17.11",
+    "lodash": "^4.17.15",
     "measure-text": "0.0.4",
     "mobxpromise": "github:cbioportal/mobxpromise#303db72588860bff0a6862a4f07a4e8a3578c94f",
     "object-sizeof": "^1.2.0",

packages/cbioportal-utils/package.json

@@ -31,7 +31,7 @@
   "dependencies": {
     "buffer": "^6.0.3",
     "genome-nexus-ts-api-client": "^1.1.20",
-    "lodash": "^4.17.11",
+    "lodash": "^4.17.15",
     "oncokb-ts-api-client": "^1.3.0",
     "superagent": "^3.8.3",
     "typescript": "4.0.3"

packages/config/jest.config.ts

@@ -6,6 +6,7 @@ const config: InitialOptionsTsJest = {
         '\\.(css|sass|less|scss)$': 'identity-obj-proxy',
         '\\.(jpg|jpeg|png|gif|eot|otf|webp|svg|ttf|woff|woff2|mp4|webm|wav|mp3|m4a|aac|oga)$':
             '<rootDir>/../config/fileMock.js',
+        'web-worker:*': 'identity-obj-proxy',
     },
     globals: {
         'ts-jest': {

packages/config/rollup.config.js

@@ -1,21 +1,21 @@
 import typescript from 'rollup-plugin-typescript2';
 import commonjs from '@rollup/plugin-commonjs';
-// import external from 'rollup-plugin-peer-deps-external';
-import autoExternal from 'rollup-plugin-auto-external';
+import externals from 'rollup-plugin-node-externals';
 import json from '@rollup/plugin-json';
 import postcss from 'rollup-plugin-postcss';
 import resolve from '@rollup/plugin-node-resolve';
 import sourcemaps from 'rollup-plugin-sourcemaps';
-import url from '@rollup/plugin-url';
+import image from '@rollup/plugin-image';
 import postcssUrl from 'postcss-url';
-import svgr from '@svgr/rollup';
+import workerLoader from 'rollup-plugin-web-worker-loader';
 
 // common rollup config options for all libraries under packages
 export default function getRollupOptions(
     input,
     mainOutput,
     moduleOutput,
-    styles
+    styles,
+    nodeExternalsOptions
 ) {
     return {
         input: input,
@@ -34,7 +34,7 @@ export default function getRollupOptions(
             },
         ],
         plugins: [
-            autoExternal(),
+            externals(nodeExternalsOptions),
             postcss({
                 autoModules: true,
                 extract: styles,
@@ -44,12 +44,12 @@ export default function getRollupOptions(
                     }),
                 ],
             }),
-            url(),
-            svgr(),
+            image(),
             typescript({
                 clean: true,
             }),
             json(),
+            workerLoader(),
             commonjs(),
             resolve(),
             sourcemaps(),

packages/oncoprintjs/LICENSE

@@ -0,0 +1,165 @@
+		GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

packages/oncoprintjs/README.md

@@ -0,0 +1,39 @@
+[![Build Status](https://travis-ci.org/cBioPortal/oncoprintjs.svg?branch=master)](https://travis-ci.org/cBioPortal/oncoprintjs)
+# OncoprintJS
+This is the library that generates the Oncoprint visualization in cBioPortal. Essentially, it populates a canvas of a grid of `m` tracks of `n` types, where each element can either be a discrete value represented by a colored glyph on a grey background or a continuous value within a color range. Oncoprint can have many conceivable uses, but in cBioPortal, it is primarily used to visualize tracks of `m` genes and `n` patient samples, where the colored glyphs represent genomic alterations. It is also used to display a heatmap of gene and/or protein expression values for those `m` genes and `n` patient samples.
+
+## Using the Node Module
+Oncoprint is on [NPM](https://www.npmjs.com/package/oncoprintjs). To install:
+
+    npm install --save oncoprintjs
+
+In order to use it, just `require` it into your script.
+
+    const Oncoprint = require('oncoprintjs');
+
+It can also be imported
+
+    import Oncoprint from "oncoprintjs";
+
+A full documentation of the API is still pending, but the typescript declarations in `dist/js/oncoprint.d.ts` may be of use.
+
+## Development
+### Getting Started
+First, clone the repo:
+
+	git clone https://github.com/cBioPortal/oncoprintjs.git
+
+Install the necessary NPM packages defined in `package.json` by running:
+
+	npm install
+
+Next, build
+
+	npm run build
+
+Which will write `dist/oncoprint.bundle.js`, which is a CommonJS module and can be included using `require`, or `import`.	
+
+The directory `rules/` contains glyph styling specifications that are specific to the genomic alterations use case of Oncoprint, which you may want to use.
+
+### Changes to Oncoprint
+If you make changes to the Oncoprint code base and want to load it into the examples, do not modify `oncoprint.bundle.js`, since all of your code will get overwritten when compiled using `npm run build`. Instead, modify the files in `src/` and then re-run `npm run build`.

packages/oncoprintjs/jest.config.ts

@@ -0,0 +1,2 @@
+import config from '../config/jest.config';
+export default config;