Examples with Arguments com.hartwig.pipeline.Arguments used on opensource projects

Example 6 with Arguments

use of com.hartwig.pipeline.Arguments in project pipeline5 by hartwigmedical.

the class GoogleComputeEngineTest method setUp.

@Before
public void setUp() throws Exception {
    images = mock(Compute.Images.class);
    imagesFromFamily = mock(Compute.Images.GetFromFamily.class);
    when(imagesFromFamily.execute()).thenReturn(new Image());
    when(images.getFromFamily(ARGUMENTS.project(), VirtualMachineJobDefinition.STANDARD_IMAGE)).thenReturn(imagesFromFamily);
    final ArgumentCaptor<Instance> instanceArgumentCaptor = ArgumentCaptor.forClass(Instance.class);
    Operation insertOperation = mock(Operation.class);
    when(insertOperation.getName()).thenReturn("insert");
    final Compute.Instances instances = mock(Compute.Instances.class);
    lifecycleManager = mock(InstanceLifecycleManager.class);
    instance = mock(Instance.class);
    when(lifecycleManager.newInstance()).thenReturn(instance);
    when(lifecycleManager.deleteOldInstancesAndStart(instanceArgumentCaptor.capture(), any(), any())).thenReturn(insertOperation);
    when(instance.getName()).thenReturn(INSTANCE_NAME);
    Compute.Instances.Stop stop = mock(Compute.Instances.Stop.class);
    Operation stopOperation = mock(Operation.class);
    when(stopOperation.getName()).thenReturn("stop");
    when(stopOperation.getStatus()).thenReturn(DONE);
    when(stop.execute()).thenReturn(stopOperation);
    when(instances.stop(ARGUMENTS.project(), FIRST_ZONE_NAME, INSTANCE_NAME)).thenReturn(stop);
    Compute.Instances.Delete delete = mock(Compute.Instances.Delete.class);
    Operation deleteOperation = mock(Operation.class);
    when(deleteOperation.getName()).thenReturn("delete");
    when(deleteOperation.getStatus()).thenReturn(DONE);
    when(delete.execute()).thenReturn(stopOperation);
    when(instances.delete(ARGUMENTS.project(), FIRST_ZONE_NAME, INSTANCE_NAME)).thenReturn(delete);
    Compute.Instances.List list = mock(Compute.Instances.List.class);
    InstanceList instanceList = mock(InstanceList.class);
    Instance one = mock(Instance.class);
    Instance two = mock(Instance.class);
    Instance three = mock(Instance.class);
    when(one.getName()).thenReturn("vm-1");
    when(two.getName()).thenReturn("vm-2");
    when(three.getName()).thenReturn("vm-3");
    List<Instance> existingInstances = Arrays.asList(one, two, three);
    when(instances.list(any(), any())).thenReturn(list);
    when(list.execute()).thenReturn(instanceList);
    when(instanceList.getItems()).thenReturn(existingInstances);
    final Compute.ZoneOperations zoneOperations = mock(Compute.ZoneOperations.class);
    final Compute.ZoneOperations.Get zoneOpGet = mock(Compute.ZoneOperations.Get.class);
    Operation zoneOpGetOperation = mock(Operation.class);
    when(zoneOpGetOperation.getStatus()).thenReturn(DONE);
    when(zoneOpGet.execute()).thenReturn(zoneOpGetOperation);
    when(zoneOperations.get(ARGUMENTS.project(), FIRST_ZONE_NAME, "insert")).thenReturn(zoneOpGet);
    when(zoneOperations.get(ARGUMENTS.project(), FIRST_ZONE_NAME, "stop")).thenReturn(zoneOpGet);
    compute = mock(Compute.class);
    when(compute.images()).thenReturn(images);
    when(compute.instances()).thenReturn(instances);
    when(compute.zoneOperations()).thenReturn(zoneOperations);
    Compute.Zones zones = mock(Compute.Zones.class);
    Compute.Zones.List zonesList = mock(Compute.Zones.List.class);
    when(zonesList.execute()).thenReturn(new ZoneList().setItems(Lists.newArrayList(zone(FIRST_ZONE_NAME), zone(SECOND_ZONE_NAME))));
    when(zones.list(ARGUMENTS.project())).thenReturn(zonesList);
    when(compute.zones()).thenReturn(zones);
    bucketWatcher = mock(BucketCompletionWatcher.class);
    victim = new GoogleComputeEngine(ARGUMENTS, compute, z -> {
    }, lifecycleManager, bucketWatcher, Labels.of(Arguments.testDefaults(), TestInputs.defaultSomaticRunMetadata()));
    runtimeBucket = MockRuntimeBucket.test();
    jobDefinition = VirtualMachineJobDefinition.builder().name("test").namespacedResults(RESULTS_DIRECTORY).startupCommand(BashStartupScript.of(runtimeBucket.getRuntimeBucket().name())).build();
}

Example 7 with Arguments

use of com.hartwig.pipeline.Arguments in project pipeline5 by hartwigmedical.

the class SmokeTest method runFullPipelineAndCheckFinalStatus.

public void runFullPipelineAndCheckFinalStatus(final String inputMode, final PipelineStatus expectedStatus, @SuppressWarnings("OptionalUsedAsFieldOrParameterType") final Optional<String> targetedRegionsBed, final RefGenomeVersion refGenomeVersion) throws Exception {
    final PipelineMain victim = new PipelineMain();
    final String version = version();
    final String setName = noDots(inputMode + "-" + version);
    final String fixtureDir = "smoke_test/" + inputMode + "/";
    @SuppressWarnings("deprecation") final String randomRunId = noDots(RandomStringUtils.random(5, true, false));
    final ImmutableArguments.Builder builder = Arguments.defaultsBuilder(Arguments.DefaultsProfile.DEVELOPMENT.toString()).sampleJson(Resources.testResource(fixtureDir + "samples.json")).cloudSdkPath(findCloudSdk()).setId(setName).runId(randomRunId).runGermlineCaller(false).cleanup(false).outputBucket("smoketest-pipeline-output-pilot-1").context(Context.DIAGNOSTIC).useTargetRegions(false).refGenomeVersion(refGenomeVersion);
    if (whoami.equals("root")) {
        String privateKeyPath = workingDir() + "/google-key.json";
        builder.privateKeyPath(privateKeyPath).uploadPrivateKeyPath(privateKeyPath);
    }
    Arguments arguments = builder.build();
    Storage storage = StorageProvider.from(arguments, CredentialProvider.from(arguments).get()).get();
    cleanupBucket(inputMode, arguments.outputBucket(), storage);
    PipelineState state = victim.start(arguments);
    assertThat(state.status()).isEqualTo(expectedStatus);
    File expectedFilesResource = new File(Resources.testResource(fixtureDir + "expected_output_files"));
    List<String> expectedFiles = FileUtils.readLines(expectedFilesResource, FILE_ENCODING);
    final String outputDir = setName + "-" + randomRunId;
    List<String> actualFiles = listOutput(outputDir, arguments.outputBucket(), storage);
    assertThat(actualFiles).containsOnlyElementsOf(expectedFiles);
    if (inputMode.equals("tumor-reference")) {
        ComparAssert.assertThat(storage, arguments.outputBucket(), outputDir).isEqualToTruthset(Resources.testResource(fixtureDir + "/truthset")).cleanup();
    }
    cleanupBucket(outputDir, arguments.outputBucket(), storage);
}

Example 8 with Arguments

use of com.hartwig.pipeline.Arguments in project pipeline5 by hartwigmedical.

the class RuntimeBucketTest method usesCmek.

@Test
public void usesCmek() {
    String keyName = "key";
    Arguments arguments = Arguments.testDefaultsBuilder().cmek(keyName).build();
    RuntimeBucket.from(storage, NAMESPACE, referenceRunMetadata(), arguments, labels);
    assertThat(bucketInfo.getValue().getDefaultKmsKeyName()).isEqualTo(keyName);
}

Example 9 with Arguments

use of com.hartwig.pipeline.Arguments in project pipeline5 by hartwigmedical.

the class FullSomaticResultsTest method setUp.

@Before
public void setUp() throws Exception {
    storage = mock(Storage.class);
    Arguments arguments = Arguments.testDefaultsBuilder().outputBucket(OUTPUT_BUCKET).build();
    victim = new FullSomaticResults(storage, arguments, 1);
    outputBucket = mock(Bucket.class);
    when(outputBucket.getName()).thenReturn(OUTPUT_BUCKET);
    when(storage.get(OUTPUT_BUCKET)).thenReturn(outputBucket);
}