Merge pull request #75 from intermine/master

Update

.github/issue_template.md

@@ -0,0 +1,20 @@
+<!--- Provide a general summary of the issue in the Title above -->
+## Description
+<!--- Provide a brief overview of the enhancement or issue. -->
+
+## Steps to Reproduce
+<!-- Please add as much detail as possible to reproduce the error/issue. -->
+
+## Expected Behaviour
+<!--- Tell us what should happen -->
+
+## Actual Behaviour
+<!--- Tell us what is happening -->
+
+## Settings
+<!-- Provide us the information of your setup -->
+- OS:
+
+## Screenshots
+<!-- If Any -->
+<!-- Show us the problem -->

.github/pull_request_template.md

@@ -0,0 +1,12 @@
+## Description
+Describe the changes made and why they were made.
+
+## Related issues and discussion
+#{Issue Number}
+
+## Screenshots, if any
+
+## Checklist
+Please make sure these boxes are checked before submitting your pull request - thanks!
+
+- [ ] Run the tests

.gitignore

@@ -63,4 +63,7 @@ typings/
 .env
 
 # next.js build output
-.next
+.next
+
+# public directory
+public/

README.md

@@ -1,28 +1,28 @@
 # InterMine Data Browser
-<p align="center">Build Status (Travis CI): <a href="https://travis-ci.org/AdrianBZG/InterMine-Data-Browser-Tool"><img src="https://travis-ci.org/AdrianBZG/InterMine-Data-Browser-Tool.svg?branch=master"></a><br>
-<p align="center"><img src="https://badges.frapsoft.com/os/v1/open-source.png?v=103"> <a href="LICENSE"><img src="https://img.shields.io/badge/License-LGPL%202.1-blue.svg"></a> <img src="https://img.shields.io/david/strongloop/express.svg"></p>
+<p align="left">Build Status (Travis CI): <a href="https://travis-ci.org/AdrianBZG/InterMine-Data-Browser-Tool"><img src="https://travis-ci.org/AdrianBZG/InterMine-Data-Browser-Tool.svg?branch=master"></a><br>
+<p align="left"><img src="https://badges.frapsoft.com/os/v1/open-source.png?v=103"> <a href="LICENSE"><img src="https://img.shields.io/badge/License-LGPL%202.1-blue.svg"></a> <img src="https://img.shields.io/david/strongloop/express.svg"></p>
 
-The goal of this project, is to implement a faceted search tool to display the data from InterMine database, allowing the users to search easily within the different mines available around InterMine. without the requirement of having an extensive knowledge of the data model.
+The goal of this project is to implement a faceted search tool to display the data from InterMine database, allowing the users to search easily within the different mines available around InterMine without the requirement of having an extensive knowledge of the data model.
 
-For the project organization, please refer to [https://github.com/intermine](https://github.com/intermine)
+For the project organization, please refer to [InterMine](https://github.com/intermine)
 
-Please note that development is very early on and the project is not ready to use yet.
+_Please note that the development is very early on and the project is not ready to use yet._
 
 ## DEPLOYMENT
 
-Try it out with the Heroku deployment (automatic deployment, may have some delay): [http://im-browser-prototype.herokuapp.com/](http://im-browser-prototype.herokuapp.com/)
+Try it out with the Heroku deployment [here](http://im-browser-prototype.herokuapp.com/) (automatic deployment, may have some delay)
 
-## DEPENDENCIES
+## GETTING STARTED
 
-Check [package.json](package.json)
+Please visit [Getting Started](getting-started.md)
 
-## BUILDING
+## DEPENDENCIES
 
-See [BUILD.md](BUILD.md)
+Check [package.json file](package.json)
 
 ## DOCUMENTATION
 
-Apart from the in-line comments in the code, documentation generated with documentation.js is available in [https://adrianbzg.github.io/InterMine-Data-Browser-Tool/](https://adrianbzg.github.io/InterMine-Data-Browser-Tool/). To update the documentation, the 'gulp documentation' is available.
+Apart from the in-line comments in the code, documentation generated with _documentation.js_ can be accessed [here](https://adrianbzg.github.io/InterMine-Data-Browser-Tool/). To update the documentation, the 'gulp documentation' is available.
 
 ## REQUIRED ONTOLOGY CONCEPTS (PER MINE) FOR EACH FILTER
 
@@ -40,18 +40,35 @@ Apart from the in-line comments in the code, documentation generated with docume
 |     Interactions     |                                         interactions.participant2.symbol + interactions.details.type + interactions.details.dataSets.name                                        |
 |      Expression      |                                 atlasExpression.pValue + atlasExpression.tStatistic + atlasExpression.expression + atlasExpression.dataSets.name                                 |
 
-## CONTRIBUTING
+## CONTRIBUTING GUIDELINES
 
 1. Find a thing to fix/implement in [Issues](https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues?direction=desc&sort=created&state=open) or come up with your own idea, [create a discussion issue](https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues/new) for it and get a feedback.
-2. [Fork the repo](https://help.github.com/articles/fork-a-repo)
-3. Create your feature branch (`git checkout -b my-new-feature`)
-4. Commit your changes (`git commit -am 'Add some feature'`)
-5. Push to the branch (`git push origin my-new-feature`)
-6. [Create new Pull Request](https://help.github.com/articles/using-pull-requests)
+
+2. [Fork](https://help.github.com/articles/fork-a-repo) the repository.
+
+3. Create your new feature branch.
+
+   ``` bash
+   git checkout -b my-new-feature
+   ```
+
+4. Commit your changes.
+
+   ``` bash
+   git commit -am 'Add some feature
+   ```
+   
+5. Push to the newly created feature branch.
+
+   ``` bash
+   git push origin my-new-feature
+   ```
+   
+6. Create a new [Pull Request](https://help.github.com/articles/using-pull-requests)
 
 ## CONTACT
 
-You can contact the developers by opening an issue in this repo.
+You can contact the developers by opening a new issue in this repository [here](https://github.com/AdrianBZG/InterMine-Data-Browser-Tool/issues/new).
 
 ## SCREENSHOTS
 

app.js

@@ -5,12 +5,6 @@ var cookieParser = require('cookie-parser');
 var logger = require('morgan');
 
 var indexRouter = require('./routes/index');
-var statisticsRouter = require('./routes/statistics');
-var fetchRouter = require('./routes/fetch');
-
-var http = require('http');
-var https = require('https');
-var fs = require('fs');
 
 var app = express();
 
@@ -25,8 +19,6 @@ app.use(cookieParser());
 app.use(express.static(path.join(__dirname, 'public')));
 
 app.use('/', indexRouter); // Home page router, to render the views
-app.use('/statistics', statisticsRouter); // Statistics router, intended to be used as REST API
-app.use('/fetch', fetchRouter); // Statistics router, intended to be used as REST API
 
 // Catch 404 and forward to error handler
 app.use(function(req, res, next) {

bin/www

@@ -25,7 +25,7 @@ var server = http.createServer(app);
  * Listen on provided port, on all network interfaces.
  */
 
-server.listen(port);
+server.listen(port, () => console.log(`Server started on http://localhost:${port}`));
 server.on('error', onError);
 server.on('listening', onListening);
 

getting-started.md

@@ -0,0 +1,59 @@
+# Getting Started with the InterMine Data Browser
+
+If you're setting up the Data Browser locally, perhaps to fix a bug or contribute a pull request, here's how you can do it.
+
+## Prerequisites
+
+A recent version of [node](https://nodejs.org/en/) and [npm](https://www.npmjs.com/)
+
+## Clone the repository to your host
+
+Head to the directory in your host machine where you want to clone/place the repository and then enter the following commands on your terminal window:
+
+``` bash
+# Clone the repository
+git clone https://github.com/intermine/InterMine-Data-Browser-Tool.git
+
+# Change present working directory
+cd InterMine-Data-Browser-Tool
+```
+
+## Install dependencies
+
+In a console, run this command from the Data Browser root folder to install all the project dependencies:
+
+``` bash
+npm install
+```
+
+## Run the tests
+
+To ensure that everything works correctly before or after some changes are made to the code base, run the tests from your console using the following command:
+
+``` bash
+npm test
+```
+
+If all the test cases run without failing then it means that you are now ready to make a pull request or can proceed further to the next step.
+
+## Launch GulpJs Tasks and Start the Data Browser server
+
+The Data Browser always runs Gulp tasks first ([gulpfile.js](gulpfile.js)) to generate all the required files related to the client-side and then runs the server. The following command needs to be entered for the same:
+
+``` bash
+# Launch the gulp default tasks (CSS, JS, Vendor, Images, Json Configs, ...) + Run the server
+npm start
+```
+If you visit [http://localhost:3000](http://localhost:3000) you should see your Data Browser running locally on your machine!
+
+## Launch GulpJs Tasks only
+
+You can run the Gulp tasks separately without running the server using the following command:
+
+``` bash
+gulp
+```
+
+Once it is completed, you can see the generated files stored inside of `public/` folder.
+
+_More information on Gulp can be obtained [here](https://gulpjs.com/)._