initial commit. fixing errors from old_master

Author: jkanche

.gitignore

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+node_modules
+dist
+build

LICENSE.md

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+CC0 1.0 Universal
+==================
+
+Statement of Purpose
+---------------------
+
+The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work").
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+
+For these and/or other purposes and motivations, and without any expectation of additional consideration or compensation, the person associating CC0 with a Work (the "Affirmer"), to the extent that he or she is an owner of Copyright and Related Rights in the Work, voluntarily elects to apply CC0 to the Work and publicly distribute the Work under its terms, with knowledge of his or her Copyright and Related Rights in the Work and the meaning and intended legal effect of CC0 on those rights.
+
+1. Copyright and Related Rights.
+--------------------------------
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+vii. other similar, equivalent or corresponding rights throughout the world based on applicable law or treaty, and any national implementations thereof.
+
+2. Waiver.
+-----------
+To the greatest extent permitted by, but not in contravention of, applicable law, Affirmer hereby overtly, fully, permanently, irrevocably and unconditionally waives, abandons, and surrenders all of Affirmer's Copyright and Related Rights and associated claims and causes of action, whether now known or unknown (including existing as well as future claims and causes of action), in the Work (i) in all territories worldwide, (ii) for the maximum duration provided by applicable law or treaty (including future time extensions), (iii) in any current or future medium and for any number of copies, and (iv) for any purpose whatsoever, including without limitation commercial, advertising or promotional purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each member of the public at large and to the detriment of Affirmer's heirs and successors, fully intending that such Waiver shall not be subject to revocation, rescission, cancellation, termination, or any other legal or equitable action to disrupt the quiet enjoyment of the Work by the public as contemplated by Affirmer's express Statement of Purpose.
+
+3. Public License Fallback.
+----------------------------
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+4. Limitations and Disclaimers.
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+d. Affirmer understands and acknowledges that Creative Commons is not a party to this document and has no duty or obligation with respect to this CC0 or use of the Work.

README.md

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+# electron epiviz app
+
+```
+download repository
+npm install && npm start
+```
+
+To build app for distribution - (builds both 32 and 64 bit versions for all platforms - linux, windows, mac os (kernel darwin and mas))
+
+`electron packager . --all  `
+
+to build using electron-builder
+
+has issues since electron-builder can't build apps for macos platform (have to build from a mac os system)
+`electron-builder .`
+
+## electron parameters
+    port = websocket port number
+    workspace = load workspace (not implemented)
+    gist = gist id (not implemented)
+
+`electron main.js --port=7123`
+
+To start loading data from local R session - 
+
+1. start epivizrStandalone.
+    TODO: update standalone open_browser to open app link. For now manually start server
+
+```
+library(epivizrStandalone)
+seqinfo <- GenomeInfoDb::Seqinfo(c("chr11","chr2"), c(1000000,8000000))
+app <- startStandalone(seqinfo=seqinfo, non_interactive=TRUE, host="localhost", verbose=TRUE)
+app$.open_browser()
+```
+
+2. start electron `electron main.js --port=7123`
+
+Then adding tracks - 
+
+```
+library(epivizr)
+data("tcga_colon_blocks")
+blocks_chart <- app$plot(tcga_colon_blocks, datasource_name="450k colon_blocks")
+```

args.js

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+'use strict'
+
+const { basename } = require('path')
+const pkg = require('./package')
+const exe = basename(process.argv[0])
+
+module.exports = require('yargs')
+  .usage(`Usage: ${exe} [options]`)
+  .strict()
+  .wrap(78)
+  .env(pkg.name.toUpperCase())
+
+  .demand(0, 1)
+
+  .option('port', {
+    alias: 'p',
+    type: 'number',
+    describe: 'Set websocket port location'
+  })
+
+.option('workspace', {
+    alias: 'p',
+    type: 'string',
+    describe: 'Load workspace'
+  })
+  
+  .help('help')
+  .version(pkg.version)
+
+  .epilogue([
+    'Environment Variables:',
+    '  NODE_ENV  Set default environment'
+  ].join('\n'))

index.html

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+<!DOCTYPE html>
+<html>
+  <head>
+    <meta charset="UTF-8">
+    <title>Hello World!</title>
+  </head>
+  <body>
+    <h1>Hello World!</h1>
+    <!-- All of the Node.js APIs are available in this renderer process. -->
+    We are using Node.js <script>document.write(process.versions.node)</script>,
+    Chromium <script>document.write(process.versions.chrome)</script>,
+    and Electron <script>document.write(process.versions.electron)</script>.
+  </body>
+
+  <script>
+    // You can also require other files to run in this process
+    require('./renderer.js')
+  </script>
+</html>

main.js

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+const electron = require('electron')
+// Module to control application life.
+const app = electron.app
+// Module to create native browser window.
+const BrowserWindow = electron.BrowserWindow
+
+const path = require('path')
+const url = require('url')
+
+const args = require('./args')
+const opts = args.parse(process.argv.slice(1))
+
+global.ARGS = opts
+
+// console.log(global.ARGS)
+
+// Keep a global reference of the window object, if you don't, the window will
+// be closed automatically when the JavaScript object is garbage collected.
+let mainWindow
+
+function createWindow () {
+  // Create the browser window.
+  mainWindow = new BrowserWindow({width: 800, height: 600})
+
+  if(opts.port) {
+    // and load the epivizr-standalone.html of the app.
+    mainWindow.loadURL(url.format({
+      pathname: path.join(__dirname, 'src/epivizr-standalone.html'),
+      protocol: 'file:',
+      slashes: true
+    }))
+
+  }
+  else {
+    // and load the index.html of the app.
+    mainWindow.loadURL(url.format({
+      pathname: path.join(__dirname, 'src/index-standalone.html'),
+      protocol: 'file:',
+      slashes: true
+    }))
+  }
+
+  // Open the DevTools.
+  mainWindow.webContents.openDevTools()
+
+  // Emitted when the window is closed.
+  mainWindow.on('closed', function () {
+    // Dereference the window object, usually you would store windows
+    // in an array if your app supports multi windows, this is the time
+    // when you should delete the corresponding element.
+    mainWindow = null
+  })
+}
+
+// This method will be called when Electron has finished
+// initialization and is ready to create browser windows.
+// Some APIs can only be used after this event occurs.
+app.on('ready', createWindow)
+
+// Quit when all windows are closed.
+app.on('window-all-closed', function () {
+  // On OS X it is common for applications and their menu bar
+  // to stay active until the user quits explicitly with Cmd + Q
+  if (process.platform !== 'darwin') {
+    app.quit()
+  }
+})
+
+app.on('activate', function () {
+  // On OS X it's common to re-create a window in the app when the
+  // dock icon is clicked and there are no other windows open.
+  if (mainWindow === null) {
+    createWindow()
+  }
+})
+
+// In this file you can include the rest of your app's specific main process
+// code. You can also put them in separate files and require them here.

package.json

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+{
+  "name": "Epiviz",
+  "version": "0.0.1",
+  "description": "Genomics Data Visualization Platform",
+  "main": "main.js",
+  "scripts": {
+    "start": "electron .",
+    "pack": "build --dir",
+    "dist": "build"
+  },
+  "build": {
+    "appId": "epiviz",
+    "mac": {
+      "category": "genomics.epiviz"
+    }
+  },
+  "repository": "https://github.com/jkanche/epiviz-electron",
+  "keywords": [
+    "epiviz",
+    "genomics",
+    "data",
+    "visualization"
+  ],
+  "postinstall": "install-app-deps",
+  "author": "Jayaram Kancherla (jkanche @ umd . edu)",
+  "license": "CC0-1.0",
+  "devDependencies": {
+    "electron": "^1.4.1",
+    "electron-builder": "^15.6.2",
+    "electron-packager": "^8.6.0"
+  },
+  "dependencies": {
+    "yargs": "^7.0.2"
+  }
+}

renderer.js

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+// This file is required by the index.html file and will
+// be executed in the renderer process for that window.
+// All of the Node.js APIs are available in this process.

src/.travis.yml

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+language: generic
+jdk:
+  - oraclejdk8
+addons:
+  apt:
+    packages:
+      - oracle-java8-installer
+script:
+  - jdk_switcher use oraclejdk8
+  - bash travis/build.sh
+env:
+  global:
+    secure: "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"

src/Dockerfile

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+FROM tutum/apache-php
+MAINTAINER "Hector Corrada Bravo" [email protected]
+
+RUN rm -fr /app
+ADD . /app

src/LICENSE

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+This package is provided to you under the terms of the Artistic License version 2.0:
+http://opensource.org/licenses/Artistic-2.0.
+
+Included below is license and copyright information for any externally
+maintained libraries used by Epiviz. All other code is Copyright (c) 2012-2015,
+Hector Corrada Bravo <[email protected]> and Florin Chelaru <[email protected]>. 
+All rights reserved.
+
+http://epiviz.cbcb.umd.edu
+http://epiviz.github.io
+http://github.com/epiviz
+
+====
+
+closure: Copyright, Google, Inc. Apache License 2.0, https://github.com/google/closure-library
+d3.js: Copyright, Michael Bostock, https://github.com/mbostock/d3
+expression-parser: Copyright, Matthew Crumley, https://github.com/silentmatt/js-expression-eval/
+file-saver: Copyright, Eli Gray,  http://eligrey.com
+jquery: Copyright, jQuery Foundation, MIT License, http://jquery.com
+DataTables: Copyright, Allan Jardine 
+dropdown-check-list: Copyright, Adrian Tosca, MIT or GPL-2 License, 
+dynatree: Copyright, Martin Wendt, MIT or GPL License, http://wwWendt.de
+farbtastic-color-picker: Copyright, Steven Wittens, GPL-2 License, 
+globalize: Copyright, Software Freedom Conservancy, Inc., MIT or GPL-2 License,  http://github.com/jquery/globalize
+parallel: Copyright, Adam Savitzky, 
+sprintf: Copyright,  Alexandru Marasteanu, 
+
+
+

src/README.md

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+Epiviz
+======
+
+Epiviz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.
+
+For more information, visit - http://epiviz.github.io/
+
+Using any PHP supported webserver
+---------------------------------
+Copy the Epiviz directory to the webserver configured directory. Navigate to <webserver-ip>/epiviz/index.php on your browser.
+
+Using PHP
+---------
+PHP (http://php.net/) lets your run local webservers. Navigate to localhost:8181 on your browser.
+To run epiviz use:
+```
+php.exe -S localhost:8181 -t <location of the epiviz directory>
+```
+
+Using Docker
+-------------------
+
+This repository includes a `Dockerfile` to run a webserver that serves
+the epiviz web application. It includes a `site-settings.js` file that
+sets up data backends pointing to the University of Maryland. Update
+that file to use a different backend. It is registered in the DockerHub
+registry: (https://hub.docker.com/r/epiviz/epiviz/)[https://hub.docker.com/r/epiviz/epiviz/].
+To run it use:
+
+```shell
+docker pull epiviz/epiviz
+docker run --name epiviz-app -d -p 80:80 epiviz/epiviz
+```