package org.ga4gh.cts.api.bioMetadata;
import com.google.protobuf.InvalidProtocolBufferException;
import com.mashape.unirest.http.exceptions.UnirestException;
import ga4gh.BioMetadataServiceOuterClass.SearchBiosamplesRequest;
import ga4gh.BioMetadataServiceOuterClass.SearchBiosamplesResponse;
import ga4gh.BioMetadataServiceOuterClass.SearchIndividualsRequest;
import ga4gh.BioMetadataServiceOuterClass.SearchIndividualsResponse;
import ga4gh.BioMetadata.*;
import org.ga4gh.ctk.transport.GAWrapperException;
import org.ga4gh.ctk.transport.URLMAPPING;
import org.ga4gh.ctk.transport.protocols.Client;
import org.ga4gh.cts.api.TestData;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import static org.assertj.core.api.Assertions.assertThat;
/**
* Tests for the BioMetadata endpoints
*/
@Category(BioMetadataTests.class)
public class BioMetadataSearchIT {
private static Client client = new Client(URLMAPPING.getInstance());
/**
* Tests the /biosamples/search endpoint to ensure that searching
* by name returns properly formed results.
* @throws GAWrapperException if the server finds the request invalid in some way
* @throws UnirestException if there's a problem speaking HTTP to the server
* @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
*/
@Test
public void checkSearchBiosamplesByName() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
// search biosamples for a known name
final SearchBiosamplesRequest req =
SearchBiosamplesRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.setName(TestData.BIOSAMPLE_NAME)
.build();
final SearchBiosamplesResponse resp = client.bioMetadata.searchBiosamples(req);
assertThat(resp.getBiosamplesCount()).isGreaterThan(0);
for (Biosample b : resp.getBiosamplesList()) {
assertThat(b.getName()).isEqualTo(TestData.BIOSAMPLE_NAME);
assertThat(b.getId()).isNotEmpty();
}
}
/**
* Tests the /biosamples/search endpoint to ensure that searching
* by individual ID returns properly formed results.
* @throws GAWrapperException if the server finds the request invalid in some way
* @throws UnirestException if there's a problem speaking HTTP to the server
* @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
*/
@Test
public void checkSearchBiosamplesByIndividual() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
// search biosamples for a known name
final SearchIndividualsRequest ireq =
SearchIndividualsRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.setName(TestData.INDIVIDUAL_NAME)
.build();
final SearchIndividualsResponse iresp = client.bioMetadata.searchIndividuals(ireq);
final String individualId = iresp.getIndividualsList().get(0).getId();
final SearchBiosamplesRequest req =
SearchBiosamplesRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.setIndividualId(individualId)
.build();
final SearchBiosamplesResponse resp = client.bioMetadata.searchBiosamples(req);
assertThat(resp).isNotNull();
for (Biosample b : resp.getBiosamplesList()) {
assertThat(b.getIndividualId()).isEqualTo(individualId);
}
}
/**
* Tests that for each Biosample returned via search there exists an
* equivalent record received by GET biosamples/id.
* @throws GAWrapperException if the server finds the request invalid in some way
* @throws UnirestException if there's a problem speaking HTTP to the server
* @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
*/
@Test
public void checkGetBiosample() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
final SearchBiosamplesRequest req =
SearchBiosamplesRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.build();
final SearchBiosamplesResponse resp = client.bioMetadata.searchBiosamples(req);
assertThat(resp).isNotNull();
for (Biosample b : resp.getBiosamplesList()) {
final Biosample found = client.bioMetadata.getBiosample(b.getId());
assertThat(found).isEqualTo(b);
}
}
/**
* Tests the /individuals/search endpoint to ensure that searching
* by name returns properly formed results.
* @throws GAWrapperException if the server finds the request invalid in some way
* @throws UnirestException if there's a problem speaking HTTP to the server
* @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
*/
@Test
public void checkSearchIndividualsByName() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
final SearchIndividualsRequest req =
SearchIndividualsRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.setName(TestData.INDIVIDUAL_NAME)
.build();
final SearchIndividualsResponse resp = client.bioMetadata.searchIndividuals(req);
assertThat(resp).isNotNull();
for (Individual i : resp.getIndividualsList()) {
assertThat(i.getName()).isEqualTo(TestData.INDIVIDUAL_NAME);
assertThat(i.getId()).isNotEmpty();
}
}
/**
* Tests that for each Individual returned via search there exists an
* equivalent record received by GET individuals/id.
* @throws GAWrapperException if the server finds the request invalid in some way
* @throws UnirestException if there's a problem speaking HTTP to the server
* @throws InvalidProtocolBufferException if there's a problem processing the JSON response from the server
*/
@Test
public void checkGetIndividual() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
final SearchIndividualsRequest req =
SearchIndividualsRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.build();
final SearchIndividualsResponse resp = client.bioMetadata.searchIndividuals(req);
assertThat(resp).isNotNull();
for (Individual i : resp.getIndividualsList()) {
final Individual found = client.bioMetadata.getIndividual(i.getId());
assertThat(found).isEqualTo(i);
}
}
}
