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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
$ git checkout release-1.1.0

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-1.1.0.jar 
-rw-r--r-- 1 user user 40K Jan  4 17:34 opencga/build/libs/opencga-client-1.1.0.jar
$ ll ~/.m2/repository/org/opencb/opencga/opencga-client/1.1.0/opencga-client-1.1.0.jar 
-rw-r--r-- 1 user user 40K Jan  4 17:34 /home/user/.m2/repository/org/opencb/opencga/opencga-client/1.1.0/opencga-client-1.1.0.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://bioinfo.hpc.cam.ac.uk/hgva/webservices/):

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

## REST client configuration options
rest:
  host: "http://bioinfo.hpc.cam.ac.uk/hgva"
  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, CohortClient 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. Please, have a look at the examples provided below.

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:

import org.opencb.commons.datastore.core.QueryOptions;
...
...
...
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. You can use the get method that the ProjectClient class inherits from the CatalogClient :

public abstract class CatalogClient<T, A> extends AbstractParentClient {
...
    public QueryResponse<T> get(String id, QueryOptions options) throws IOException
...
}

Inputs:

  • id: String containing the project alias or project name. You can get available project alias at the Datasets and Studies section.
  • options: must be set to null in this case, since no filtering options are available for this purpose.

For example, getting all metadata for the reference_grch37 project:

openCGAClient.getProjectClient().get("reference_grch37", null);

Getting all metadata from all studies associated to a particular project. You can use the getStudies method of the ProjectClient:

public class ProjectClient extends CatalogClient<Project, Project> {
...
    public QueryResponse<Study> getStudies(String projectId, QueryOptions options) throws CatalogException, IOException
...
}

Inputs:

  • projectId: String containing the project alias or project name. You can get available project alias at the Datasets and Studies section.
  • options: QueryOptions object which will contain the pairs (filter, value) that form the query. QueryOptions objects work as a Map object, by providing a put method that enables to add the (filter, value) pairs. Available filters and possible values for them are those described at the Swagger specification for the corresponding web service.

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

import org.opencb.commons.datastore.core.QueryOptions;
...
...
...
QueryOptions queryOptions = new QueryOptions();
openCGAClient.getProjectClient().getStudies("cancer_grch37", queryOptions);

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. You can use the search method of the StudyClient class:

public class StudyClient extends CatalogClient<Study, StudyAclEntry> {
...
    public QueryResponse<Study> search(Query query, QueryOptions options) throws IOException
...
}

Inputs:

  • query: Query object which will contain the pairs (filter, value) that form the query. Query objects work as a Map object, by providing a put method that enables to add the (filter, value) pairs. Available filters and possible values for them are those described at the Swagger specification for the corresponding web service.
  • options: not necessary, can be set to an empty QueryOptions.

For example, getting all metadata for all available studies:

import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
...
...
...
Query query = new Query();
QueryOptions queryOptions = new QueryOptions();
openCGAClient.getStudyClient().search(query, queryOptions);

Getting summary data from a particular study. You can use the getSummary method of the StudyClient class:

public class StudyClient extends CatalogClient<Study, StudyAclEntry> {
...
    public QueryResponse<StudySummary> getSummary(String studyId, QueryOptions options) throws CatalogException, IOException
...
}

Inputs:

  • studyId: String containing the study alias or study name. You can get available study aliases/names by using the method above.
  • options: QueryOptions object which will contain the pairs (filter, value) that form the query. QueryOptions objects work as a Map object, by providing a put method that enables to add the (filter, value) pairs. Available filters and possible values for them are those described at the Swagger specification for the corresponding web service.

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

import org.opencb.commons.datastore.core.QueryOptions;
...
...
...
QueryOptions queryOptions = new QueryOptions();
openCGAClient.getStudyClient().getSummary("reference_grch37:1kG_phase3", queryOptions);


Getting all available metadata for a particular study. You can use the get method that the class StudyClient inherits from the CatalogClient class:

public abstract class CatalogClient<T, A> extends AbstractParentClient {
...
    public QueryResponse<T> get(String id, QueryOptions options) throws IOException
...
}

Inputs:

  • id: String containing the study alias or study name. You can get available study aliases calling the search method of the StudyClient.
  • options: must be set to null in this case, since no filtering options are available for this purpose.

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

openCGAClient.getStudyClient().get("GONL", null);

Getting all samples metadata for a given study. You can use the method getSamples of the StudyClient class:

public class StudyClient extends CatalogClient<Study, StudyAclEntry> {
...
    public QueryResponse<Sample> getSamples(String studyId, QueryOptions options) throws CatalogException, IOException
...
}

Inputs:

  • studyId: String containing the study alias or study name. You can get available study aliases/names by using the method above.
  • options: QueryOptions object which will contain the pairs (filter, value) that form the query. QueryOptions objects work as a Map object, by providing a put method that enables to add the (filter, value) pairs. Available filters and possible values for them are those described at the Swagger specification for the corresponding web service.

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.

import org.opencb.commons.datastore.core.QueryOptions;
...
...
...
QueryOptions queryOptions = new QueryOptions();
openCGAClient.getStudyClient().getSummary("reference_grch37:1kG_phase3", queryOptions);

Getting information about samples

Get all metadata for a particular sample. You can use the get method that the class SampleClient inherits from CatalogClient class:

public abstract class CatalogClient<T, A> extends AbstractParentClient {
...
    public QueryResponse<T> get(String id, QueryOptions options) throws IOException
...
}

Inputs:

  • id: String containing the sample name. You can get available samples by using some of the methods described above.
  • options: must be set to null in this case, since no filtering options are available for this purpose.

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

openCGAClient.getSampleClient().get("HG00096", null);

Getting information about cohorts

Getting all samples metadata in a given cohort. You can use the getSamples method of the CohortClient:

public class CohortClient extends AnnotationClient<Cohort, CohortAclEntry> {
...
    public QueryResponse<Sample> getSamples(String cohortId, QueryOptions options) throws CatalogException, IOException
...
}

Inputs:

  • cohortId: String containing the cohort id.
  • options: QueryOptions object which will contain the pairs (filter, value) that form the query. QueryOptions objects work as a Map object, by providing a put method that enables to add the (filter, value) pairs. Available filters and possible values for them are those described at the Swagger specification for the corresponding web service.

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

import org.opencb.commons.datastore.core.QueryOptions;
...
...
...
QueryOptions queryOptions = new QueryOptions();
queryOptions.put("study", "reference_grch37:1kG_phase3");
openCGAClient.getCohortClient().getSamples("GBR", queryOptions);

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