Initial commit

.eslintrc

+{
+  "globals": {
+    "db": true,
+    "acl": true
+  },
+  "extends": ["standard", "standard-react"],
+  "ecmaFeatures": {
+    "jsx": true
+  },
+  "plugins": [
+    "react"
+  ]
+}

.gitignore

+.DS_Store
+node_modules/
+api/db/*
+public/assets/*
+.idea

README.md

+# JATS Writer
+
+Powered by PubSweet.
+
+# Preconditions
+
+Node.js, version must be of 4.x.x series, is a requirement, read about how to install it here: [https://nodejs.org/en/](https://nodejs.org/en/)
+
+Warning about `npm`: Because the newly released npm 3 changed the way npm installs nested dependencies (it flattens them), and we rely on previous behaviour (https://github.com/npm/npm/issues/9809) please use npm 2.x while we work on resolving this.
+
+# Install
+
+```bash
+$ git clone https://gitlab.coko.foundation/jgutix/jats-writer.git
+$ cd jats-writer
+$ npm install
+```
+
+# Start the server
+
+First, initialize your blog by running and going through the setup process:
+```bash
+$ NODE_ENV=dev npm run setup
+```
+
+To start the JS compilation and webserver, run:
+```bash
+$ npm run dev
+```
+
+Point your browser to: [http://localhost:3000/manage/posts](http://localhost:3000/manage/posts) and login with the chosen admin username and password and all should be well. Visit [http://localhost:3000](http://localhost:3000) for the blog landing page.
+
+# Themes
+
+Themes are a PubSweet component. If you want to write a custom theme, set your theme component in `config.js`. When you require a style from a component, using e.g. `import './Signup.scss'` in `app/components/Signup/Signup.jsx`, we'll automatically find the right themed style (e.g. `app/components/PepperTheme/Signup/Signup.scss` if theme is set to `PepperTheme`). You can then continue working on your themed styles as usual, and the page will hot-reload when you change anything.
+
+# How to look into the database for debugging purposes
+
+Run a PouchDB server (comes with the app):
+```bash
+$ npm run pouchdb
+```
+
+And navigate to [http://localhost:5984/_utils/](http://localhost:5984/_utils/). Click "Add New Database" and enter "dev", to connect to the development database. You should now be able to run queries on your development database.
+
+# Production installation
+
+These are instructions for Ubuntu 15.10, exact steps may vary from OS to OS so if you're using another system, please take this as general guidance only.
+
+First [install node 4.x](https://github.com/nodesource/distributions#debinstall)
+
+```bash
+curl -sL https://deb.nodesource.com/setup_4.x | sudo -E bash -
+sudo apt-get install -y nodejs
+```
+
+Then clone the repository:
+
+```bash
+git clone https://gitlab.coko.foundation/jgutix/jats-writer.git
+```
+
+Install the required npm modules:
+
+```bash
+npm install
+```
+
+Build the production JS:
+
+```bash
+npm run build
+```
+
+Configure your initial admin account:
+
+```bash
+NODE_ENV=production npm run setup
+```
+
+Start the server:
+
+```bash
+npm run start
+```
+
+The application should now be accessible through port 80 on your server.

app/app.js

+import React from 'react'
+import ReactDOM from 'pubsweet-core/node_modules/react-dom'
+
+import configureStore from 'pubsweet-core/app/store/configureStore'
+import Root from 'pubsweet-core/app/components/Root'
+
+import { AppContainer } from 'pubsweet-core/node_modules/react-hot-loader'
+import { browserHistory } from 'pubsweet-core/node_modules/react-router'
+import { syncHistoryWithStore } from 'pubsweet-core/node_modules/react-router-redux'
+
+let store = configureStore(browserHistory, {})
+let history = syncHistoryWithStore(browserHistory, store)
+
+const rootEl = document.getElementById('root')
+
+ReactDOM.render(
+  <AppContainer>
+    <Root store={store} history={history}/>
+  </AppContainer>,
+  rootEl
+)
+
+if (module.hot) {
+  module.hot.accept('pubsweet-core/app/components/Root', () => {
+    const NextRoot = require('pubsweet-core/app/components/Root').default
+    ReactDOM.render(
+      <AppContainer>
+        <NextRoot store={store} history={history}/>
+      </AppContainer>,
+      rootEl
+    )
+  })
+}

app/components/Navigation/Navigation.jsx

+import React from 'react'
+import { LinkContainer } from 'pubsweet-core/node_modules/react-router-bootstrap'
+import { Navbar, Nav, NavItem, NavbarBrand } from 'pubsweet-core/node_modules/react-bootstrap'
+
+import AuthHelper from 'pubsweet-core/app/helpers/AuthHelper'
+import NavbarUser from 'pubsweet-core/app/components/Navigation/NavbarUser'
+
+export default class Navigation extends React.Component {
+
+  render () {
+    const { actions, auth } = this.props
+    let logoutButtonIfAuthenticated
+    if (auth.isAuthenticated) {
+      logoutButtonIfAuthenticated = <NavbarUser
+        roles={auth.roles}
+        username={auth.username}
+        switchRole={actions.switchRole}
+        onLogoutClick={actions.logoutUser}
+      />
+    }
+    return (
+      <Navbar fluid>
+        <Navbar.Header>
+          <NavbarBrand>
+            <a href='#'><img src='/pubsweet.jpg' alt='science'/></a>
+          </NavbarBrand>
+        </Navbar.Header>
+        <Nav eventKey={0}>
+          <LinkContainer to='/manage/posts'>
+            <NavItem>Science Posts</NavItem>
+          </LinkContainer>
+          { AuthHelper.showForUser(auth, 'users') &&
+            <LinkContainer to='/manage/users'>
+              <NavItem>Users</NavItem>
+            </LinkContainer>
+          }
+        </Nav>
+        { logoutButtonIfAuthenticated }
+      </Navbar>
+    )
+  }
+}
+
+Navigation.propTypes = {
+  actions: React.PropTypes.object.isRequired,
+  auth: React.PropTypes.object
+}

app/components/Scientist/PubsweetXMLStore.js

+'use strict'
+
+var oo = require('substance-scientist/node_modules/substance/util/oo')
+var request = require('substance-scientist/node_modules/substance/util/request')
+
+function PubsweetXMLStore () {
+
+}
+
+PubsweetXMLStore.Prototype = function () {
+  this.readXML = function (documentId, cb) {
+    var cached = localStorage.getItem(documentId)
+    if (cached) {
+      return cb(null, cached)
+    }
+    request('GET', '/data/' + documentId + '.xml', null, cb)
+  }
+
+  // TODO make functional
+  this.writeXML = function (documentId, xml, cb) {
+    localStorage.setItem(documentId, xml)
+    cb(null)
+  }
+}
+
+oo.initClass(PubsweetXMLStore)
+
+module.exports = PubsweetXMLStore

app/components/Scientist/ReactScientistWriter.jsx

+var React = require('react')
+var ReactDOM = require('pubsweet-core/node_modules/react-dom')
+
+import { bindActionCreators } from 'pubsweet-core/node_modules/redux'
+import { connect } from 'pubsweet-core/node_modules/react-redux'
+import * as Actions from 'pubsweet-core/app/actions'
+var Editor = require('substance-scientist/examples/jats-editor/JATSEditor.js')
+var Configurator = require('substance-scientist/packages/common/BaseConfigurator')
+var Component = require('substance-scientist/node_modules/substance/ui/Component')
+var DocumentSession = require('substance-scientist/node_modules/substance/model/DocumentSession')
+var request = require('substance-scientist/node_modules/substance/util/request')
+
+var PublisherPackage = require('substance-scientist/packages/publisher/package')
+var PubsweetXMLStore = require('./PubsweetXMLStore')
+var path = require('path')
+
+// Jats-editor wrapped in a React component
+// ------------------
+
+class ReactScientistWriter extends React.Component {
+
+  getWriter () {
+    return this
+  }
+
+  createDocumentSession () {
+    return new DocumentSession('')
+  }
+
+  // New props arrived, update the editor
+  componentDidUpdate () {
+    var documentSession = this.createDocumentSession()
+
+    this.writer.extendProps({
+      documentSession: documentSession
+    })
+  }
+
+  save (source, changes, callback) {
+    // var exporter = new LensArticleExporter()
+    // this.props.onSave(exporter.exportDocument(source), callback)
+    console.log('do nothing for now')
+  }
+
+  componentDidMount () {
+    var self = this
+    PubsweetXMLStore.prototype.readXML = function(documentId, cb) {
+      if (self.props.fragment && self.props.fragment.source) {
+        return cb(null, self.props.fragment.source)
+      }
+      return cb(null,
+          '<?xml version="1.0" encoding="UTF-8"?>' +
+          '<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.1d3 20150301//EN"  "JATS-archivearticle1.dtd">' +
+          '<article article-type="sample" dtd-version="1.1d3" xmlns:xlink="http://www.w3.org/1999/xlink">' +
+            '<front>' +
+              '<article-meta></article-meta>' +
+            '</front>' +
+            '<body><p id="p1">Empty Sample</p></body>' +
+            '<back></back>' +
+          '</article>')
+
+      }
+    PubsweetXMLStore.prototype.writeXML = function (documentId, xml, cb) {
+      self.props.onSave(xml, cb)
+    }
+
+    var el = ReactDOM.findDOMNode(this)
+
+    var configurator = new Configurator({
+      name: 'pubsweet-jats-editor',
+      configure: function (config) {
+        // Base package with regular JATS support
+        config.import(PublisherPackage)
+
+        // Define XML Store
+        config.setXMLStore(PubsweetXMLStore)
+        config.addStyle(path.join(__dirname, 'ScientistWriter.scss'))
+      }
+    })
+
+    this.writer = Component.mount(Editor, {
+      documentId: 'vanilla',
+      configurator: configurator
+    }, el)
+  }
+
+  componentWillUnmount () {
+    this.writer.dispose()
+  }
+
+  render () {
+
+    let editor
+
+    if (this.props.fragment) {
+      editor = React.DOM.div({
+        className: 'scientist-writer-wrapper'
+      })
+    } else {
+      editor = <p>Loading</p>
+    }
+
+    return (
+        <div>
+          {editor}
+        </div>
+    )
+  }
+}
+
+ReactScientistWriter.propTypes = {
+  fragment: React.PropTypes.object,
+  id: React.PropTypes.string.isRequired,
+  onSave: React.PropTypes.func
+}
+
+function mapStateToProps (state, ownProps) {
+  return {
+    id: ownProps.id,
+    fragment: _.find(state.fragments, function (f) {
+      return f.id === ownProps.id
+    })
+  }
+}
+
+function mapDispatchToProps (dispatch) {
+  return {
+    actions: bindActionCreators(Actions, dispatch)
+  }
+}
+
+export default connect(
+    mapStateToProps,
+    mapDispatchToProps
+)(ReactScientistWriter)

app/components/Scientist/ScientistWriter.jsx

+import React from 'react'
+import ReactScientistWriter from './ReactScientistWriter'
+import { bindActionCreators } from 'pubsweet-core/node_modules/redux'
+import { connect } from 'pubsweet-core/node_modules/react-redux'
+import * as Actions from 'pubsweet-core/app/actions'
+
+// Styles
+import './ScientistWriter.scss'
+
+class ScientistWriter extends React.Component {
+  constructor (props) {
+    super(props)
+    this.save = this.save.bind(this)
+    this.uploadFile = this.uploadFile.bind(this)
+  }
+
+  save (source, callback) {
+    let doc = Object.assign(this.props.fragment, {
+      source: source
+    })
+    this.props.actions.updateFragment(doc)
+
+    callback(null, source)
+  }
+
+  uploadFile (file, callback) {
+    return this.props.uploadFile(file, callback)
+  }
+
+  render () {
+    return <ReactScientistWriter
+      documentId={this.props.fragment.id}
+      id={this.props.fragment.id}
+      version={this.props.fragment.version}
+      content={this.props.fragment.source}
+      onSave={this.save}
+      />
+  }
+}
+
+ScientistWriter.propTypes = {
+  fragment: React.PropTypes.object,
+  actions: React.PropTypes.object,
+  save: React.PropTypes.func,
+  uploadFile: React.PropTypes.func,
+  id: React.PropTypes.string.isRequired
+}
+
+// export default ScientistWriter
+function mapStateToProps (state, ownProps) {
+  return {
+    id: ownProps.params.id,
+    fragment: _.find(state.fragments, function (f) {
+      return f.id === ownProps.params.id
+    })
+  }
+}
+
+function mapDispatchToProps (dispatch) {
+  return {
+    actions: bindActionCreators(Actions, dispatch)
+  }
+}
+
+export default connect(
+    mapStateToProps,
+    mapDispatchToProps
+)(ScientistWriter)

app/index.ejs

+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+  <title><%= htmlWebpackPlugin.options.title %></title>
+</head>
+<body>
+  <div id="root"></div>
+</body>
+</html>

app/index.html

+<html>
+<head>
+  <title>JATS Editor</title>
+  <meta charset="UTF-8">
+  <script type="text/javascript" src="/assets/app.js" async="async"></script>
+
+</head>
+<body>
+<div id="root"></div>
+</body>
+</html>
\ No newline at end of file

app/routes.jsx

+import React from 'react'
+import { Route } from 'pubsweet-core/node_modules/react-router'
+
+import { requireAuthentication } from 'pubsweet-core/app/components/AuthenticatedComponent'
+
+// Manage
+import Manage from 'pubsweet-core/app/components/Manage/Manage'
+import PostsManager from 'pubsweet-core/app/components/PostsManager/PostsManager'
+import ScientistWriter from '../app/components/Scientist/ScientistWriter'
+import UsersManager from 'pubsweet-core/app/components/UsersManager/UsersManager'
+
+// Public
+import Blog from 'pubsweet-core/app/components/Blog/Blog'
+
+// Authentication
+import Login from 'pubsweet-core/app/components/Login/Login'
+import Signup from 'pubsweet-core/app/components/Signup/Signup'
+
+export default (
+  <Route>
+    <Route path='/' component={Blog}/>
+
+    <Route path='/manage' component={requireAuthentication(Manage)}>
+      <Route path='posts' component={PostsManager} />
+      <Route path='sciencewriter/:id' component={ScientistWriter} />
+      <Route path='users' component={UsersManager} />
+    </Route>
+
+    <Route path='/login' component={Login} />
+    <Route path='/signup' component={Signup} />
+  </Route>
+)

bin/www

+const api = require('pubsweet-core/api/api')
+const http = require('http')
+// Get port from environment or default to 3000
+var port = process.env.PORT || '3000'
+api.set('port', port)
+
+var server = http.createServer(api)
+
+server.listen(port)
+server.on('error', onError)
+server.on('listening', onListening)
+
+function onError (error) {
+  throw error
+}
+
+function onListening () {
+  var addr = server.address()
+  console.log('PubSweet is listening on ' + addr.port)
+}

config.js

+module.exports = {
+  secret: 'EXAMPLEDONTUSE',
+  API_ENDPOINT: '/api',
+  theme: 'PepperTheme',
+  editor: 'app/components/Scientist/ScientistWriter.jsx',
+  routes: 'app/routes.jsx',
+  navigation: 'app/components/Navigation/Navigation.jsx'
+}

package.json

+{
+  "name": "jats-writer",
+  "version": "0.0.1-alpha1",
+  "private": true,
+  "scripts": {
+    "setup": "node node_modules/pubsweet-core/api/setup.js",
+    "build": "webpack --colors --config ./webpack/webpack.prod.config.js",
+    "start": "PORT=80 NODE_ENV=production node bin/www",
+    "dev": "NODE_ENV=dev LOADER=hot node bin/www",
+    "pouchdb": "./node_modules/pubsweet-core/node_modules/pouchdb-server/bin/pouchdb-server --level-prefix=./api/db/ -d ./api/db/",
+    "test": "NODE_ENV=test ./node_modules/.bin/mocha --harmony api/test/*.js -R nyan",
+    "eslint": "eslint"
+  },
+  "dependencies": {
+    "pubsweet-core": "git+https://gitlab.coko.foundation/pubsweet/core.git#7a8e4ee",
+    "scientist": "git+https://github.com/substance/scientist.git#v1.0.0-alpha"
+  },
+  "devDependencies": {
+    "babel-core": "^6.3.0",
+    "babel-loader": "^6.2.4",
+    "babel-eslint": "^4.1.3",
+    "babel-preset-react-hmre": "^1.1.1",
+    "babel-preset-es2015": "^6.6.0",
+    "babel-preset-react": "^6.5.0",
+    "babel-preset-stage-2": "^6.5.0",
+    "css-loader": "^0.23.1",
+    "eslint": "^1.10.3",
+    "eslint-config-standard": "^4.4.0",
+    "eslint-config-standard-react": "^1.2.1",
+    "eslint-loader": "^1.2.0",
+    "eslint-plugin-react": "^3.14.0",
+    "eslint-plugin-standard": "^1.1.0",
+    "extract-text-webpack-plugin": "^1.0.1",
+    "react": "^0.14.7",
+    "sass-loader": "^3.2.0",
+    "style-loader": "^0.12.3",
+    "url-loader": "^0.5.7",
+    "webpack": "^1.12.14",
+    "webpack-dev-middleware": "^1.6.1",
+    "webpack-hot-middleware": "^2.10.0"
+  },
+  "standard": {
+    "parser": "babel-eslint"
+  }
+}
\ No newline at end of file

webpack/webpack.dev.config.js

+var path = require('path')
+var webpack = require('webpack')
+var config = require('../config')
+var ThemeResolver = require('pubsweet-core/webpack/ThemeResolver')
+var assetsPath = path.join(__dirname, '..', 'public', 'assets')
+var publicPath = '/assets/'
+
+// We're including JSX components from our components package,
+// but excluding its node_modules.
+var commonLoaders = [
+  {
+    test: /\.js$|\.jsx$/,
+    loader: 'babel',
+    query: {
+      presets: ['react-hmre', 'es2015', 'react', 'stage-2'],
+      plugins: ['pubsweet-core/node_modules/react-hot-loader/babel']
+    },
+    include: [
+      new RegExp(path.join(__dirname, '../node_modules/pubsweet-core/app')),
+      new RegExp(path.join(__dirname, '../app')),
+      new RegExp(path.join(__dirname, '../../core/app')) // TODO: Temp while linked.
+    ]
+  },
+  { test: /\.png$/, loader: 'url-loader' },
+  {
+    test: /\.woff|\.woff2|\.svg|.eot|\.ttf/,
+    loader: 'url?prefix=font/&limit=10000'
+  },
+  { test: /\.html$/, loader: 'html-loader' },
+  { test: /\.json$/, loader: 'json-loader' },
+  { test: /\.css$|\.scss$/,
+    exclude: /\.local\.s?css$/, // Exclude local styles from global
+    loader: 'style-loader!css-loader!sass-loader'
+  },
+  { test: /\.css$|\.scss$/,
+    include: /\.local\.s?css/, // Local styles
+    loader: 'style-loader!css-loader?modules&importLoaders=1!sass-loader'
+  }
+
+]
+
+module.exports = [