Using the JavaScript REST client

OpencgaClient is the Javascript client library for OpenCGA RESTful Web Services, all the web services are accessible through this client, and it offers a quick way to query OpenCGA projects through web interface. In the same way than in  Using RESTful Web Services URL tutorial, we will focus on those end points more interesting for HGVA users. In order to make it easy to follow we will use the same examples used in Using RESTful Web Services URL.

Configuring and initializing the client

There are two javascript files that need to be imported - opencga-client-config.js and opencga-client.js.

OpenCGA Client expects an OpenCGA Client Configuration to initialise and create the client. The configuration object is of the following structure

this.opencgaClientConfig = new OpenCGAClientConfig("bioinfo.hpc.cam.ac.uk/hgva", "v1", false, "hgva");

Arguments of OpencgaClientConfig 

• Host - The host name is given here. In our case, It is the HGVA host.  
• Version - Version number
• UseCookies - Cookies are used to store user ID and session ID. They are not needed in HGVA as The data is open to public. Hence It is set to false.
• CookiePrefix - Prefix is used in case we are using cookies. This can be set anything as the user wishes. 
  

OpenCGA Client can be created with the above opencgaClientConfig.

this.opencgaClient = new OpenCGAClient(this.opencgaClientConfig);

Getting information about genomic variants

The then and catch clauses are used as opencgaClient returns responses as Javascript Promises.

this.opencgaClient.studies().getVariants(id, params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});

Getting information about projects

Method to call for gettting information about projects

this.opencgaClient.projects().info(id, params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});

Method to call for getting studies belonging to the project

this.opencgaClient.projects().getStudies(id, params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});

Getting information about studies

Method to call for getting all metadata for all available studies

this.opencgaClient.studies().search(params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});

Method to call for getting summary data for a study whose ID must be passed as a parameter

this.opencgaClient.studies().summary(id, params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});

Method to call for getting all metadata for a study 

this.opencgaClient.studies().info(id, params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});

Method to call for getting all samples metadata for a study 

this.opencgaClient.studies().getSamples(id, params, options)
	.then(function(response) {
		Correct response is captured here
	})
	.catch(function(response) {
		Error response is captured here
	});