cBioPortal · alisman · Jun 8, 2022 · Jul 6, 2015 · Jul 7, 2015 · Jul 7, 2015
diff --git a/.prettierignore b/.prettierignore
@@ -19,11 +19,13 @@
 *.ejs
 *.toml
 *.xml
+*.py
 *module.scss.d.ts
 **/generated/**
 src/shared/lib/oql/oql-parser.js
 packages/**/dist/**
 yarn.lock
+LICENSE
 .prettierignore
 .DS_Store
 .gitignore

diff --git a/package.json b/package.json
@@ -85,11 +85,10 @@
     "@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",
@@ -222,7 +221,7 @@
     "object-sizeof": "^1.2.0",
     "oncokb-styles": "~1.3.0",
     "oncokb-ts-api-client": "^1.3.1",
-    "oncoprintjs": "5.0.4",
+    "oncoprintjs": "^6.0.0-beta.0",
     "pako": "2.0.2",
     "parameter-validator": "^1.0.2",
     "path-browserify": "^1.0.1",
@@ -295,11 +294,12 @@
     "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",

diff --git a/packages/cbioportal-frontend-commons/package.json b/packages/cbioportal-frontend-commons/package.json
@@ -41,7 +41,7 @@
     "cbioportal-utils": "^0.3.20",
     "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",

diff --git a/packages/cbioportal-utils/package.json b/packages/cbioportal-utils/package.json
@@ -31,7 +31,7 @@
   "dependencies": {
     "buffer": "^6.0.3",
     "genome-nexus-ts-api-client": "^1.1.22",
-    "lodash": "^4.17.11",
+    "lodash": "^4.17.15",
     "oncokb-ts-api-client": "^1.3.1",
     "superagent": "^3.8.3",
     "typescript": "4.0.3"

diff --git a/packages/config/jest.config.ts b/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': {

diff --git a/packages/config/rollup.config.js b/packages/config/rollup.config.js
@@ -1,21 +1,22 @@
 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 +35,7 @@ export default function getRollupOptions(
             },
         ],
         plugins: [
-            autoExternal(),
+            externals(nodeExternalsOptions),
             postcss({
                 autoModules: true,
                 extract: styles,
@@ -44,12 +45,12 @@ export default function getRollupOptions(
                     }),
                 ],
             }),
-            url(),
-            svgr(),
+            image(),
             typescript({
                 clean: true,
             }),
             json(),
+            workerLoader(),
             commonjs(),
             resolve(),
             sourcemaps(),

diff --git a/packages/oncoprintjs/LICENSE b/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
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+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
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+   b) under the GNU GPL, with none of the additional permissions of
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+  3. Object Code Incorporating Material from Library Header Files.
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+   a) Give prominent notice with each copy of the object code that the
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diff --git a/packages/oncoprintjs/README.md b/packages/oncoprintjs/README.md
@@ -0,0 +1,73 @@
+[![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.
+
+### Using a local version of oncoprintjs during development (e.g. in cBioPortal)
+
+yalc (https://github.com/wclr/yalc) is extremely useful for this.
+
+Whenever you have made a change to oncoprintjs you want to bring into another package:
+(1) First navigate to the oncoprint directory. Then build:
+
+	npm run build
+
+(2) Then "publish" the package locally using yalc
+
+	yalc publish
+
+(3) Now go to the directory of your project (e.g. cbioportal-frontend), and add the local package
+
+	yalc add oncoprintjs
+
+(4) Install packages again, using npm or yarn. Now, you will be using your local version of oncoprintjs.
+
+(5) When you no longer want to be using the local version of oncoprintjs, simply run
+
+	yalc remove oncoprintjs
+
+And run npm or yarn again.
+
+### 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`.
+
+### Schematic diagrams
+oncoprintjs is written loosely with a Model-View-Controller framework, although some Views definitely have their own state.
+
+![image](https://user-images.githubusercontent.com/636232/163244642-6ef2c80e-a0b5-43d6-ab95-24b8f8a4a2a3.png)
+
+![image](https://user-images.githubusercontent.com/636232/163244709-cbe64929-e650-44cd-a579-2de3294dccc0.png)
+
+
diff --git a/packages/oncoprintjs/jest.config.ts b/packages/oncoprintjs/jest.config.ts
@@ -0,0 +1,2 @@
+import config from '../config/jest.config';
+export default config;
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		import config from '../config/jest.config';
		export default config;