PRIDE Cluster web-app

A web application for the EBI PRIDE Cluster resource. We use mostly AngularJS as a framework for a JavaEE container-based web app. For visualisation NVD3 and Angularjs-nvd3-directives are used.

In-dev prototype deployed here: http://wwwdev.ebi.ac.uk/pride/cluster.

Project structure

The web application code is contained within the app folder inside src/main/webapp. The structure is as follows:

app.js

Defines the main application context and modules dependencies. The index.html files defines the main layout, including the EBI Frontier template.

/views

Defines main views and routing, as well as html files for templating and data binding. Each main view can use different AngularJS directives. These are defined within the components folder.

/components

Defines AngularJS directives and services. Each component folder is names as componentName-componentType. For example the folder clusterDetail-directive contains code that defines the <prc-cluster-detail/> directive and the folder cluster-service contains code defining the Cluster service to retrieve data from the PRIDE Cluster web-service.

Directives

<prc-cluster-detail>

Displays information about a given cluster specified by its attribute clusterid.

<prc-cluster-list>

Displays a list of cluster summaries for a given query and sortField attributes.

Services

ClusterService

Provides methods to query the PRIDE Cluster web-service at the clustersummary and clusterdetail end points.

Build cycle

Install Dependencies

There are two kinds of dependencies in this project: tools and angular framework code. The tools help us manage and test the application.

• We get the tools we depend upon via npm, the [node package manager][npm].
• We get the angular code via bower, a [client-side code package manager][bower].

npm has been pre-configured in package/json to automatically run bower so we can simply do:

npm install

Behind the scenes this will also call bower install. Once this is done, you should find that you have two new folders in your project.

• node_modules - contains the npm packages for the tools we need
• src/main/webapp/bower_components - contains the angular framework files

Note that the bower_components folder would normally be installed in the root folder but angular-seed changes this location through the .bowerrc file. Putting it in the app folder makes it easier to serve the files by a webserver.

Run the Application

We have preconfigured the project with a simple development web server. The simplest way to start this server is:

npm start

Now browse to the app at http://localhost:8000/index.html. Right now, in order to see any data we need to deploy the PRIDE Cluster WS locally and have it producing some data. This is something to change in the near future.

Testing

Running Unit Tests

The angular-seed app comes preconfigured with unit tests. These are written in [Jasmine][jasmine], which we run with the [Karma Test Runner][karma]. We provide a Karma configuration file to run them.

• the configuration is found at karma.conf.js
• the unit tests are found next to the code they are testing and are named as ..._test.js.

The easiest way to run the unit tests is to use the supplied npm script:

npm test

This script will start the Karma test runner to execute the unit tests. Moreover, Karma will sit and watch the source and test files for changes and then re-run the tests whenever any of them change. This is the recommended strategy; if your unit tests are being run every time you save a file then you receive instant feedback on any changes that break the expected code functionality.

You can also ask Karma to do a single run of the tests and then exit. This is useful if you want to check that a particular version of the code is operating as expected. The project contains a predefined script to do this:

npm run test-single-run

Updating Angular

Since the angular framework library code and tools are acquired through package managers (npm and bower) you can use these tools instead to update the dependencies.

You can update the tool dependencies by running:

npm update

This will find the latest versions that match the version ranges specified in the package.json file.

You can update the Angular dependencies by running:

bower update

This will find the latest versions that match the version ranges specified in the bower.json file.

Continuous Integration

Travis CI

[Travis CI][travis] is a continuous integration service, which can monitor GitHub for new commits to your repository and execute scripts such as building the app or running tests. The PRIDE cluster webapp project contains a Travis configuration file, .travis.yml, which will cause Travis to run the tests when pushed to GitHub. The results can be seen here.