From c75dd1a55ab7a5ae22ff381058950a630bdab65a Mon Sep 17 00:00:00 2001
From: Adam Abeshouse <adamabeshouse@gmail.com>
Date: Fri, 25 Aug 2017 16:57:05 -0400
Subject: [PATCH] Merge pull request #29 from pambot/node-package

Updates to node package functionality
---
 packages/oncoprintjs/.npmignore   |  8 ++++++++
 packages/oncoprintjs/.travis.yml  |  3 +++
 packages/oncoprintjs/README.md    | 24 +++++++++++++++---------
 packages/oncoprintjs/gulpfile.js  | 10 ++++++----
 packages/oncoprintjs/package.json |  6 +++---
 5 files changed, 35 insertions(+), 16 deletions(-)

diff --git a/packages/oncoprintjs/.npmignore b/packages/oncoprintjs/.npmignore
index a2424b16386..f13f1eb96ef 100644
--- a/packages/oncoprintjs/.npmignore
+++ b/packages/oncoprintjs/.npmignore
@@ -1,5 +1,13 @@
 # Created by https://www.gitignore.io
 
+### Repo Files ###
+src/
+test/
+server.js
+gulpfile.js
+.gitignore
+.travis.yml
+
 ### Node ###
 # Logs
 logs
diff --git a/packages/oncoprintjs/.travis.yml b/packages/oncoprintjs/.travis.yml
index 214d9ab472e..866614d575a 100644
--- a/packages/oncoprintjs/.travis.yml
+++ b/packages/oncoprintjs/.travis.yml
@@ -3,6 +3,9 @@ node_js:
 - '6'
 before_deploy:
 - npm run build
+- mv ./dist/oncoprint-bundle.js ./index.js
+- cp -r ./dist/* ./
+- rm -rf dist
 deploy:
   provider: npm
   email: cbioportal@gmail.com
diff --git a/packages/oncoprintjs/README.md b/packages/oncoprintjs/README.md
index 97773282ce5..dd0cc2b7cda 100644
--- a/packages/oncoprintjs/README.md
+++ b/packages/oncoprintjs/README.md
@@ -2,7 +2,19 @@
 # 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.
 
-## Getting Started
+## 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');
+
+This will load the `Oncoprint` prototype into your environment. A full documentation of the API is still pending, but to see the basic usage in action, please follow the instructions below and take a look at the examples in the `test/` directory.
+
+## Development
+### Getting Started
 First, clone the repo:
 
 	git clone https://github.com/cBioPortal/oncoprintjs.git
@@ -11,20 +23,14 @@ Install the necessary NPM packages defined in `package.json`, create the output
 
 	cd oncoprintjs
 	npm install
-	mkdir -p dist
 	gulp
 
-Oncoprint currently has some hard-coded image files, so to set it up for the examples, run:
-
-	mkdir -p dist/img
-	mv dist/*.svg dist/img
-
 You should now have a folder `dist/` with the oncoprint files in it, including `oncoprint-bundle.js`. This is the original library file. The directory `rules/` contains glyph styling specifications that are specific to the genomic alterations use case of Oncoprint, so it is separate for the library file. 
 
-## Changes to Oncoprint
+### 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 gulped. Instead, modify the files in `src/` and then re-run `gulp`.
 
-## Minimum Working Example
+### Minimum Working Example
 The `test/` folder holds the code that runs the examples. All examples are mounted in `index.html`, which contains one JS file per example. The file `server.js` starts the basic node server, serving files from `dist/`, `rules/`, and `test/` on port 3000. To see the examples, execute the following:
 
 	node server.js
diff --git a/packages/oncoprintjs/gulpfile.js b/packages/oncoprintjs/gulpfile.js
index 0e68b02e7e9..a5ee3058ccf 100644
--- a/packages/oncoprintjs/gulpfile.js
+++ b/packages/oncoprintjs/gulpfile.js
@@ -1,7 +1,9 @@
 var gulp = require('gulp');
 var shell = require('gulp-shell');
 
-gulp.task('default', shell.task(['browserify src/js/main.js -o dist/oncoprint-bundle.js',
-				'cp src/css/* dist/',
-				'cp src/img/* dist/',
-				]));
+gulp.task('default', shell.task([
+	'mkdir -p dist/img',
+	'browserify src/js/main.js -o dist/oncoprint-bundle.js',
+	'cp src/css/* dist/',
+	'cp src/img/* dist/img/',
+]));
diff --git a/packages/oncoprintjs/package.json b/packages/oncoprintjs/package.json
index c6080f6ae73..a2c26e68ecf 100644
--- a/packages/oncoprintjs/package.json
+++ b/packages/oncoprintjs/package.json
@@ -3,8 +3,8 @@
   "version": "1.0.2",
   "description": "A data visualization for cancer genomic data.",
   "scripts": {
-      "clean": "rm -rf dist",
-      "build": "npm run clean && mkdir -p dist && gulp && mkdir -p dist/img && mv dist/*.svg dist/img"
+    "clean": "rm -rf dist",
+    "build": "npm run clean && gulp"
   },
   "repository": {
     "type": "git",
@@ -43,7 +43,7 @@
   "dependencies": {
     "express": "^4.15.3",
     "gl-matrix": "^2.3.2",
-    "jquery": "^1.11.1",
+    "jquery": "^1.11.3",
     "underscore": "^1.7.0"
   }
 }