Examples with Sample com.hartwig.patient.Sample used on opensource projects

Example 1 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class BwaAligner method run.

public AlignmentOutput run(final SingleSampleRunMetadata metadata) throws Exception {
    StageTrace trace = new StageTrace(NAMESPACE, metadata.sampleName(), StageTrace.ExecutorType.COMPUTE_ENGINE).start();
    RuntimeBucket rootBucket = RuntimeBucket.from(storage, NAMESPACE, metadata, arguments, labels);
    Sample sample = sampleSource.sample(metadata);
    if (sample.bam().isPresent()) {
        String noPrefix = sample.bam().orElseThrow().replace("gs://", "");
        int firstSlash = noPrefix.indexOf("/");
        String bucket = noPrefix.substring(0, firstSlash);
        String path = noPrefix.substring(firstSlash + 1);
        return AlignmentOutput.builder().sample(metadata.sampleName()).status(PipelineStatus.PROVIDED).maybeAlignments(GoogleStorageLocation.of(bucket, path)).build();
    }
    final ResourceFiles resourceFiles = buildResourceFiles(arguments);
    sampleUpload.run(sample, rootBucket);
    List<Future<PipelineStatus>> futures = new ArrayList<>();
    List<GoogleStorageLocation> perLaneBams = new ArrayList<>();
    List<ReportComponent> laneLogComponents = new ArrayList<>();
    List<GoogleStorageLocation> laneFailedLogs = new ArrayList<>();
    for (Lane lane : sample.lanes()) {
        RuntimeBucket laneBucket = RuntimeBucket.from(storage, laneNamespace(lane), metadata, arguments, labels);
        BashStartupScript bash = BashStartupScript.of(laneBucket.name());
        InputDownload first = new InputDownload(GoogleStorageLocation.of(rootBucket.name(), fastQFileName(sample.name(), lane.firstOfPairPath())));
        InputDownload second = new InputDownload(GoogleStorageLocation.of(rootBucket.name(), fastQFileName(sample.name(), lane.secondOfPairPath())));
        bash.addCommand(first).addCommand(second);
        bash.addCommands(OverrideReferenceGenomeCommand.overrides(arguments));
        SubStageInputOutput alignment = new LaneAlignment(arguments.sbpApiRunId().isPresent(), resourceFiles.refGenomeFile(), first.getLocalTargetPath(), second.getLocalTargetPath(), metadata.sampleName(), lane).apply(SubStageInputOutput.empty(metadata.sampleName()));
        perLaneBams.add(GoogleStorageLocation.of(laneBucket.name(), resultsDirectory.path(alignment.outputFile().fileName())));
        bash.addCommands(alignment.bash()).addCommand(new OutputUpload(GoogleStorageLocation.of(laneBucket.name(), resultsDirectory.path()), RuntimeFiles.typical()));
        futures.add(executorService.submit(() -> runWithRetries(metadata, laneBucket, VirtualMachineJobDefinition.alignment(laneId(lane).toLowerCase(), bash, resultsDirectory))));
        laneLogComponents.add(new RunLogComponent(laneBucket, laneNamespace(lane), Folder.from(metadata), resultsDirectory));
        laneFailedLogs.add(GoogleStorageLocation.of(laneBucket.name(), RunLogComponent.LOG_FILE));
    }
    AlignmentOutput output;
    if (lanesSuccessfullyComplete(futures)) {
        List<InputDownload> laneBams = perLaneBams.stream().map(InputDownload::new).collect(Collectors.toList());
        BashStartupScript mergeMarkdupsBash = BashStartupScript.of(rootBucket.name());
        laneBams.forEach(mergeMarkdupsBash::addCommand);
        SubStageInputOutput merged = new MergeMarkDups(laneBams.stream().map(InputDownload::getLocalTargetPath).filter(path -> path.endsWith("bam")).collect(Collectors.toList())).apply(SubStageInputOutput.empty(metadata.sampleName()));
        mergeMarkdupsBash.addCommands(merged.bash());
        mergeMarkdupsBash.addCommand(new OutputUpload(GoogleStorageLocation.of(rootBucket.name(), resultsDirectory.path()), RuntimeFiles.typical()));
        PipelineStatus status = runWithRetries(metadata, rootBucket, VirtualMachineJobDefinition.mergeMarkdups(mergeMarkdupsBash, resultsDirectory));
        ImmutableAlignmentOutput.Builder outputBuilder = AlignmentOutput.builder().sample(metadata.sampleName()).status(status).maybeAlignments(GoogleStorageLocation.of(rootBucket.name(), resultsDirectory.path(merged.outputFile().fileName()))).addAllReportComponents(laneLogComponents).addAllFailedLogLocations(laneFailedLogs).addFailedLogLocations(GoogleStorageLocation.of(rootBucket.name(), RunLogComponent.LOG_FILE)).addReportComponents(new RunLogComponent(rootBucket, Aligner.NAMESPACE, Folder.from(metadata), resultsDirectory));
        if (!arguments.outputCram()) {
            outputBuilder.addReportComponents(new SingleFileComponent(rootBucket, Aligner.NAMESPACE, Folder.from(metadata), bam(metadata.sampleName()), bam(metadata.sampleName()), resultsDirectory), new SingleFileComponent(rootBucket, Aligner.NAMESPACE, Folder.from(metadata), bai(bam(metadata.sampleName())), bai(bam(metadata.sampleName())), resultsDirectory)).addDatatypes(new AddDatatype(DataType.ALIGNED_READS, metadata.barcode(), new ArchivePath(Folder.from(metadata), BwaAligner.NAMESPACE, bam(metadata.sampleName()))), new AddDatatype(DataType.ALIGNED_READS_INDEX, metadata.barcode(), new ArchivePath(Folder.from(metadata), BwaAligner.NAMESPACE, bai(metadata.sampleName()))));
        }
        output = outputBuilder.build();
    } else {
        output = AlignmentOutput.builder().sample(metadata.sampleName()).status(PipelineStatus.FAILED).build();
    }
    trace.stop();
    executorService.shutdown();
    return output;
}

Example 2 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class LocalSomaticMetadataTest method setUp.

@Before
public void setUp() throws Exception {
    setId = "setId";
    tumorName = "CORE123T";
    refName = "CORE123R";
    jsonSampleSource = mock(JsonSampleSource.class);
    tumorSample = mock(Sample.class);
    final Sample refSample = mock(Sample.class);
    stagedOutputPublisher = mock(StagedOutputPublisher.class);
    victim = new LocalSomaticMetadata(Arguments.testDefaultsBuilder().setId(setId).build(), jsonSampleSource, stagedOutputPublisher);
    when(jsonSampleSource.sample(SampleType.REFERENCE)).thenReturn(Optional.of(refSample));
    when(tumorSample.name()).thenReturn(tumorName);
    when(refSample.name()).thenReturn(refName);
}

Example 3 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class JsonSampleSourceTest method simplePairParsedAndTumorReturned.

@Test
public void simplePairParsedAndTumorReturned() {
    JsonSampleSource victim = new JsonSampleSource(Resources.testResource("json_sample_source/single_lane.json"));
    Sample sample = victim.sample(TestInputs.tumorRunMetadata());
    assertThat(sample.name()).isEqualTo("CPCT12345678T");
    assertThat(sample.lanes()).hasSize(1);
    Lane lane = sample.lanes().get(0);
    assertThat(lane.firstOfPairPath()).isEqualTo("CPCT12345678T_R1.fastq");
    assertThat(lane.secondOfPairPath()).isEqualTo("CPCT12345678T_R2.fastq");
    assertThat(lane.laneNumber()).isEqualTo("1");
}

Example 4 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class JsonSampleSourceTest method simplePairParsedAndReferenceReturned.

@Test
public void simplePairParsedAndReferenceReturned() {
    JsonSampleSource victim = new JsonSampleSource(Resources.testResource("json_sample_source/single_lane.json"));
    Sample sample = victim.sample(TestInputs.referenceRunMetadata());
    assertThat(sample.name()).isEqualTo("CPCT12345678R");
    assertThat(sample.lanes()).hasSize(1);
    Lane lane = sample.lanes().get(0);
    assertThat(lane.firstOfPairPath()).isEqualTo("CPCT12345678R_R1.fastq");
    assertThat(lane.secondOfPairPath()).isEqualTo("CPCT12345678R_R2.fastq");
    assertThat(lane.laneNumber()).isEqualTo("1");
}

Example 5 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class SbpSampleReaderTest method parsesPatientNameFromReadsFile.

@Test
public void parsesPatientNameFromReadsFile() {
    returnJson(FASTQ_JSON);
    Sample sample = victim.read(EXISTS);
    assertThat(sample.name()).isEqualTo(SAMPLE_NAME);
}