package org.ga4gh.cts.api.reads;
import com.google.protobuf.InvalidProtocolBufferException;
import com.mashape.unirest.http.exceptions.UnirestException;
import org.ga4gh.ctk.CtkLogs;
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.ga4gh.cts.api.Utils;
import ga4gh.ReadServiceOuterClass.*;
import ga4gh.Reads.*;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import java.net.HttpURLConnection;
import java.util.Collections;
import java.util.List;
import java.util.stream.Collectors;
import java.util.stream.IntStream;
import static org.assertj.core.api.Assertions.assertThat;
import static org.ga4gh.cts.api.Utils.aSingle;
import static org.ga4gh.cts.api.Utils.catchGAWrapperException;
import static org.ga4gh.cts.api.Utils.getReadGroupId;
/**
* Verify that data returned from <tt>/reads/search</tt> queries meets expectations.
*/
@Category(ReadsTests.class)
public class ReadsSearchIT implements CtkLogs {
private static Client client = new Client(URLMAPPING.getInstance());
/**
* Call <tt>/reads/search</tt> with a range that contains zero reads, and verify that it returns none.
* (Adapted from an old JavaScript test.)
*
* @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 searchRangeWithNoReadsReturnsZeroResults() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
final String refId = Utils.getValidReferenceId(client);
final long emptyRangeStart = 0; // is this range actually empty?
final long emptyRangeEnd = 100;
final SearchReadsRequest srReq =
SearchReadsRequest.newBuilder()
.setReferenceId(refId)
.addAllReadGroupIds(aSingle(getReadGroupId(client)))
.setStart(emptyRangeStart)
.setEnd(emptyRangeEnd)
.build();
final SearchReadsResponse srResp = client.reads.searchReads(srReq);
final List<ReadAlignment> alignments = srResp.getAlignmentsList();
assertThat(alignments).isEmpty();
}
/**
* Call <tt>/reads/search</tt> with a range that contains multiple reads, and verify
* they are well-formed.
* (Adapted from an old JavaScript test.)
*
* @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 searchReadsProducesWellFormedReads() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
// first get a valid reference
final String refId = Utils.getValidReferenceId(client);
final long start = 150;
final long end = 160;
final SearchReadsRequest srReq =
SearchReadsRequest.newBuilder()
.setReferenceId(refId)
.addAllReadGroupIds(aSingle(getReadGroupId(client)))
.setStart(start)
.setEnd(end)
.build();
final SearchReadsResponse srResp = client.reads.searchReads(srReq);
final List<ReadAlignment> alignments = srResp.getAlignmentsList();
alignments.stream().forEach(read -> assertThat(read.getNextMatePosition()).isNotNull());
alignments.stream()
.forEach(read -> assertThat(read.getNextMatePosition()
.getReferenceName()).isEqualTo(TestData.REFERENCE_NAME));
alignments.stream().forEach(read -> assertThat(read.getAlignment()).isNotNull());
alignments.stream().forEach(read -> assertThat(read.getAlignment().getCigarList()).isNotNull());
}
/**
* Fetch every {@link ReadGroupSet} named in {@link TestData#EXPECTED_READGROUP_NAMES} using
* <tt>searchReadGroupSets</tt> and verify that it returns the expected {@link ReadGroupSet}.
*
* @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 searchReadGroupSetsMustReturnReadGroupSetsWithExpectedNames() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
for (String expectedReadGroupSetName : TestData.EXPECTED_READGROUPSETS_NAMES) {
final SearchReadGroupSetsRequest req =
SearchReadGroupSetsRequest.newBuilder()
.setDatasetId(TestData.getDatasetId())
.setName(expectedReadGroupSetName)
.build();
final SearchReadGroupSetsResponse resp = client.reads.searchReadGroupSets(req);
final List<ReadGroupSet> readGroupSets = resp.getReadGroupSetsList();
assertThat(readGroupSets).hasSize(1);
final ReadGroupSet readGroupSet = readGroupSets.get(0);
assertThat(readGroupSet.getName()).isEqualTo(expectedReadGroupSetName);
assertThat(readGroupSet.getDatasetId()).isEqualTo(TestData.getDatasetId());
}
}
/**
* Verify that passing zero read group names in a {@link SearchReadsRequest} fails.
*
* @throws Exception if there's a problem we didn't catch
*/
@SuppressWarnings("ThrowableResultOfMethodCallIgnored")
@Test
public void searchReadsWithNoIdsFails() throws Exception {
// first get a valid reference
final String refId = Utils.getValidReferenceId(client);
final SearchReadsRequest request =
SearchReadsRequest.newBuilder()
.addAllReadGroupIds(Collections.emptyList())
.setStart(0L)
.setEnd(150L)
.setReferenceId(refId)
.build();
final GAWrapperException t = catchGAWrapperException(() -> client.reads.searchReads(request));
assertThat(t.getHttpStatusCode()).isEqualTo(HttpURLConnection.HTTP_BAD_REQUEST);
}
/**
* Verify that passing one read group name in a {@link SearchReadsRequest}
* returns valid reads.
*
* @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 searchReadsWithOneReadGroupIdSucceeds() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
// first get a valid reference
final String refId = Utils.getValidReferenceId(client);
// get a ReadGroup id
final String readGroupId = getReadGroupId(client);
final SearchReadsRequest request =
SearchReadsRequest.newBuilder()
.addAllReadGroupIds(aSingle(readGroupId))
.setStart(0L)
.setEnd(150L)
.setReferenceId(refId)
.build();
final SearchReadsResponse response = client.reads.searchReads(request);
assertThat(response.getAlignmentsList()).isNotNull();
response.getAlignmentsList().stream()
.forEach(readAlignment ->
assertThat(readAlignment.getAlignedSequence()).isNotNull()
.matches(TestData.ALIGNED_SEQUENCE_CONTENTS_PATTERN));
}
/**
* Verify that passing all known read group names in a {@link SearchReadsRequest}
* returns all matching read groups.
*
* @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 searchReadsWithAllIdsReturnsReadsForEach() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
// first get a valid reference
final String refId = Utils.getValidReferenceId(client);
// get all ReadGroupSets
final List<ReadGroupSet> allReadGroupSets = Utils.getAllReadGroupSets(client);
// collect all IDs from the ReadGroups
final List<String> allReadGroupIds =
allReadGroupSets.stream()
.flatMap(readGroupSet ->
readGroupSet.getReadGroupsList()
.stream())
.map(ReadGroup::getId)
.collect(Collectors.toList());
final SearchReadsRequest request =
SearchReadsRequest.newBuilder()
.addAllReadGroupIds(allReadGroupIds)
.setStart(0L)
.setEnd(150L)
.setReferenceId(refId)
.build();
final SearchReadsResponse response = client.reads.searchReads(request);
assertThat(response.getAlignmentsList()).isNotNull();
response.getAlignmentsList().stream()
.forEach(readAlignment ->
assertThat(readAlignment.getAlignedSequence()).isNotNull()
.matches(TestData.ALIGNED_SEQUENCE_CONTENTS_PATTERN));
}
/**
* <p>Verify aligned sequences contain only the permitted symbols.</p>
* <p>In any {@link ReadAlignment} in our compliance test data,
* the <tt>alignedSequence</tt> field can only contain
* {@link TestData#ALIGNED_SEQUENCE_CONTENTS_PATTERN}.
*
* @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 readsResponseMatchesACTGNPattern() throws InvalidProtocolBufferException, UnirestException, GAWrapperException {
final String refId = Utils.getValidReferenceId(client);
for (String readGroupSetName : TestData.EXPECTED_READGROUPSETS_NAMES) {
for (String readGroupName : TestData.EXPECTED_READGROUPSET_READGROUP_NAMES.get(readGroupSetName)) {
final String readGroupId = Utils.getReadGroupIdForName(client, readGroupSetName, readGroupName);
final SearchReadsRequest request =
SearchReadsRequest.newBuilder()
.addAllReadGroupIds(aSingle(readGroupId))
.setReferenceId(refId)
.setStart(0L)
.setEnd(150L)
.build();
final SearchReadsResponse response = client.reads.searchReads(request);
assertThat(response.getAlignmentsList()).isNotNull();
response.getAlignmentsList().stream()
.forEach(readAlignment ->
assertThat(readAlignment.getAlignedSequence()).isNotNull()
.matches(TestData.ALIGNED_SEQUENCE_CONTENTS_PATTERN));
}
}
}
/**
* Verifies that a request for all the readGroupIds in a Read Group Set
* returns only alignments with those readgroupIds.
*
* @throws Exception if there's a problem
*/
@Test
public void testSearchReadsMultipleReadGroupsInReadGroupSet() throws Exception {
final String referenceId = Utils.getValidReferenceId(client);
final List<ReadGroupSet> allReadGroupSets = Utils.getAllReadGroupSets(client);
final ReadGroupSet readGroupSet = allReadGroupSets.get(0);
final List<ReadGroup> readGroups = readGroupSet.getReadGroupsList();
final List<String> readGroupIds = readGroups
.stream()
.map(readGroup -> readGroup.getId())
.collect(Collectors.toList());
SearchReadsRequest.Builder builder = SearchReadsRequest.newBuilder();
IntStream.range(0, readGroupIds.size()).forEach(index -> builder.addReadGroupIds(readGroupIds.get(index)));
final SearchReadsRequest request = builder
.setStart(0L)
.setEnd(150L)
.setReferenceId(referenceId)
.build();
final SearchReadsResponse response = client.reads.searchReads(request);
assertThat(response.getAlignmentsList()).isNotNull();
for (ReadAlignment readAlignment : response.getAlignmentsList()) {
final String readGroupId = readAlignment.getReadGroupId();
assertThat(readGroupId).isIn(readGroupIds);
assertThat(readAlignment.getAlignedSequence()).isNotNull()
.matches(TestData.ALIGNED_SEQUENCE_CONTENTS_PATTERN);
}
}
}
