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The Java client provides an API to the whole OpenCGA RESTful layer. We will here only focus on those methods which are of most interest for HGVA users. In order to understand how to create queries using these methods, it would be interesting to have a look at the Datasets and Studies section before.

Getting the Java client code

As previously said, the Java client code is distributed together with the rest of the OpenCGA code

The OpenCGA code can be cloned in your machine by executing in your terminal:

$ git clone https://github.com/opencb/opencga.git

Alternatively, you can download tar.gz files with the code for the latest tags/releases of OpenCGA from:

https://github.com/opencb/opencga/releases

Once you have downloaded the code, follow the instructions at the How to Build section of the OpenCGA repository:

https://github.com/opencb/opencga

That will generate the .jar containing the Java client library. If you are using Maven as a build and dependency manager you shall find the client .jar file at:

$ ll opencga/build/libs/opencga-client-1.0.0-rc3.jar 
-rw-r--r-- 1 user user 40K Jan  4 17:34 opencga/build/libs/opencga-client-1.0.0-rc3.jar
$ ll ~/.m2/repository/org/opencb/opencga/opencga-client/1.0.0-rc3/opencga-client-1.0.0-rc3.jar 
-rw-r--r-- 1 user user 40K Jan  4 17:34 /home/user/.m2/repository/org/opencb/opencga/opencga-client/1.0.0-rc3/opencga-client-1.0.0-rc3.jar

Initializing the Java client

The OpenCGAClient constructor requires a ClientConfiguration object to be passed as a parameter. This ClientConfiguration object will contain basic connection details, namely the URL that points to HGVA web services. The best way to obtain a ClientConfiguration object is to create a .yml configuration file that will later be passed to the load static method of the ClientConfiguration class to generate a new ClientConfiguration object. A client-configuration.yml template is provided within the OpenCGA code. If you have cloned the OpenCGA code, you will find the client-configuration.yml file at:

$ ll opencga/opencga-client/src/main/resources/client-configuration.yml 
-rw-r--r-- 1 user user 272 Sep  8 14:10 opencga/opencga-client/src/main/resources/client-configuration.yml

This file can easily be edited to set the rest→host attribute to the HGVA web services URL (http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/):

client-configuration.yml
---
## number of seconds that session remain open
sessionDuration: 12000

## REST client configuration options
rest:
  host: "http://bioinfodev.hpc.cam.ac.uk/hgva-1.0"
  batchQuerySize: 200
  timeout: 10000
  defaultLimit: 2000

## gRPC configuration options
grpc:
  host: "localhost:9091"

Once the client-configuration.yml file is ready, you can just create an OpenCGAClient object by running:

import org.opencb.opencga.client.rest.OpenCGAClient;
import org.opencb.opencga.client.config.ClientConfiguration;
...
...
...
OpenCGAClient openCGAClient;
ClientConfiguration clientConfiguration;


// Load client configuration from client-configuration.yml file
clientConfiguration = ClientConfiguration.load(new FileInputStream(Paths.get("/path/to/client-configuration.yml")));
// Create OpenCGA client
openCGAClient = new OpenCGAClient(clientConfiguration);

The OpenCGAClient will, in turn, be able to generate different data client types that will provide methods for accessing the different data types. The most relevant data client types for HGVA users will be the VariantClient, ProjectClient, StudyClient and SampleClient, that you can create by simply doing:

VariantClient variantClient = openCGAClient.getVariantClient();
ProjectClient projectClient = openCGAClient.getProjectClient();
StudyClient studyClient = openCGAClient.getStudyClient();
SampleClient sampleClient = openCGAClient.getSampleClient();

Through these clients you will be able to access information about variants, projects, studies and samples.

Getting information about genomic variants

Getting variant data from a given study: you can use the query method within the VariantClient class:

public class VariantClient extends AbstractParentClient {
...
    public QueryResponse<Variant> query(ObjectMap params) throws CatalogException, IOException 
...
}

The params parameter can be provided as a QueryOptions object, which works as a Map by providing a put method that enables to add pairs (filter, value) that form the actual query. Available filters and possible values for them are those described at the Swagger specification for the corresponding web service. For example, get TTN variants from the Genome of the Netherlands study, which is framed within the reference_grch37 project. We will also limit the number of returned results to 3:

QueryOptions queryOptions = new QueryOptions();
queryOptions.put("gene", "TTN");
queryOptions.put("studies", "GONL");
queryOptions.put("limit", 3);
openCGAClient.getVariantClient().query(queryOptions);


Getting information about projects

Getting all metadata from a particular project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/info

For example, getting all metadata for the reference_grch37 project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/reference_grch37/info

Getting all metadata from all studies associated to a particular project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/{projects}/studies

For example, getting all studies and their metadata for the cancer_grch37 project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/projects/cancer_grch37/studies

Getting information about studies

Get all available studies and their metadata. Please note, of special interest will be here the field alias which contains the study identifier to be used as an input whenever a study must be passed as a parameter:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search

For example, getting all metadata for all available studies:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/search

Getting summary data from a particular study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/summary

For example, getting summary data for study 1kG_phase3 which is framed within project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37:1kG_phase3/summary

Getting all available metadata for a particular study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/info

For example, getting all metadata for study GONL  which is framed within the project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37:GONL/info

Getting all samples metadata for a given study:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/{project}:{study}/samples

For example, getting all samples metadata for study 1kG_phase3 which is framed within project reference_grch37. Please, note that not all studies contain samples data, e.g. GONL, ExAC, among others, only provide variant lists and aggregated frequencies, i.e. no sample genotypes.

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/studies/reference_grch37:1kG_phase3/samples

Getting information about samples

Get all metadata for a particular sample:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/{sample}/info?study={project}:{study}

For example, get all metadata for sample HG00096 of the 1kG_phase3 study which is framed within the reference_grch37 project:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/samples/HG00096/info?study=reference_grch37:1kG_phase3

Getting information about cohorts

Getting all samples metadata in a given cohort:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/{cohort}/samples?study={project}:{study}

For example, get all samples metadata for cohort GBR from study 1kG_phase3 which is framed within project reference_grch37:

http://bioinfodev.hpc.cam.ac.uk/hgva-1.0/webservices/rest/v1/cohorts/GBR/samples?study=reference_grch37:1kG_phase3

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