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Example 1 with JsonKey

use of com.hartwig.platinum.iam.JsonKey in project platinum by hartwigmedical.

the class KubernetesEngine method findOrCreate.

public KubernetesCluster findOrCreate(final String runName, final List<TumorNormalPair> pairs, final JsonKey jsonKey, final String outputBucketName, final String serviceAccountEmail) {
    try {
        String clusterName = configuration.cluster().orElse(runName);
        GcpConfiguration gcpConfiguration = configuration.gcp();
        String parent = String.format("projects/%s/locations/%s", gcpConfiguration.projectOrThrow(), gcpConfiguration.regionOrThrow());
        if (find(fullPath(gcpConfiguration.projectOrThrow(), gcpConfiguration.regionOrThrow(), clusterName)).isEmpty()) {
            create(containerApi, parent, clusterName, gcpConfiguration);
        }
        if (!configuration.inCluster()) {
            if (!processRunner.execute(of("gcloud", "container", "clusters", "get-credentials", clusterName, "--region", gcpConfiguration.regionOrThrow(), "--project", gcpConfiguration.projectOrThrow()))) {
                throw new RuntimeException("Failed to get credentials for cluster");
            }
            if (!processRunner.execute(of("kubectl", "get", "configmaps"))) {
                throw new RuntimeException("Failed to run kubectl command against cluster");
            }
            LOGGER.info("Connection to cluster {} configured via gcloud and kubectl", Console.bold(clusterName));
        }
        DefaultKubernetesClient kubernetesClient = new DefaultKubernetesClient();
        TargetNodePool targetNodePool = configuration.gcp().nodePoolConfiguration().map(c -> TargetNodePool.fromConfig(c, configuration.batch().map(BatchConfiguration::size).orElse(configuration.samples().isEmpty() ? configuration.sampleIds().size() : configuration.samples().size()))).orElse(TargetNodePool.defaultPool());
        if (!targetNodePool.isDefault()) {
            new GcloudNodePool(processRunner).create(targetNodePool, serviceAccountEmail, clusterName, gcpConfiguration.projectOrThrow());
        }
        return new KubernetesCluster(runName, new JobScheduler(kubernetesClient, configuration.retryFailed()), new PipelineServiceAccountSecretVolume(jsonKey, kubernetesClient, "service-account-key"), new PipelineConfigMapVolume(pairs, kubernetesClient, runName), outputBucketName, serviceAccountEmail, configuration, Delay.threadSleep(), targetNodePool);
    } catch (Exception e) {
        throw new RuntimeException("Failed to create cluster", e);
    }
}
Also used : IPAllocationPolicy(com.google.api.services.container.v1beta1.model.IPAllocationPolicy) NodePool(com.google.api.services.container.v1beta1.model.NodePool) LoggerFactory(org.slf4j.LoggerFactory) NodeConfig(com.google.api.services.container.v1beta1.model.NodeConfig) Duration.ofSeconds(java.time.Duration.ofSeconds) Container(com.google.api.services.container.v1beta1.Container) JsonKey(com.hartwig.platinum.iam.JsonKey) List.of(java.util.List.of) GoogleJsonResponseException(com.google.api.client.googleapis.json.GoogleJsonResponseException) Operation(com.google.api.services.container.v1beta1.model.Operation) BatchConfiguration(com.hartwig.platinum.config.BatchConfiguration) DefaultKubernetesClient(io.fabric8.kubernetes.client.DefaultKubernetesClient) GcpConfiguration(com.hartwig.platinum.config.GcpConfiguration) TumorNormalPair(com.hartwig.platinum.p5sample.TumorNormalPair) PlatinumConfiguration(com.hartwig.platinum.config.PlatinumConfiguration) Console(com.hartwig.platinum.Console) Logger(org.slf4j.Logger) IOException(java.io.IOException) RetryPolicy(net.jodah.failsafe.RetryPolicy) Cluster(com.google.api.services.container.v1beta1.model.Cluster) Failsafe(net.jodah.failsafe.Failsafe) Create(com.google.api.services.container.v1beta1.Container.Projects.Locations.Clusters.Create) List(java.util.List) Get(com.google.api.services.container.v1beta1.Container.Projects.Locations.Clusters.Get) CreateClusterRequest(com.google.api.services.container.v1beta1.model.CreateClusterRequest) PrivateClusterConfig(com.google.api.services.container.v1beta1.model.PrivateClusterConfig) Duration.ofMinutes(java.time.Duration.ofMinutes) Optional(java.util.Optional) BatchConfiguration(com.hartwig.platinum.config.BatchConfiguration) GcpConfiguration(com.hartwig.platinum.config.GcpConfiguration) GoogleJsonResponseException(com.google.api.client.googleapis.json.GoogleJsonResponseException) IOException(java.io.IOException) DefaultKubernetesClient(io.fabric8.kubernetes.client.DefaultKubernetesClient)

Example 2 with JsonKey

use of com.hartwig.platinum.iam.JsonKey in project platinum by hartwigmedical.

the class Platinum method run.

public void run() {
    LOGGER.info("Starting platinum run with name {} and input {}", Console.bold(runName), Console.bold(input));
    GcpConfiguration gcpConfiguration = configuration.gcp();
    PipelineServiceAccount serviceAccount = PipelineServiceAccount.from(iam, resourceManager, runName, gcpConfiguration.projectOrThrow(), configuration);
    String serviceAccountEmail = serviceAccount.findOrCreate();
    ServiceAccountPrivateKey privateKey = ServiceAccountPrivateKey.from(configuration, iam);
    JsonKey jsonKey = privateKey.create(gcpConfiguration.projectOrThrow(), serviceAccountEmail);
    List<TumorNormalPair> pairs = DecomposeSamples.apply(configuration.sampleBucket().map(b -> new SampleBucket(storage.get(b)).apply()).orElseGet(configuration::samples));
    int submitted = kubernetesEngine.findOrCreate(runName, pairs, jsonKey, OutputBucket.from(storage).findOrCreate(runName, gcpConfiguration.regionOrThrow(), serviceAccountEmail, configuration), serviceAccountEmail).submit(samples(configuration, pairs, runName));
    LOGGER.info("Platinum started {} pipelines on GCP", Console.bold(String.valueOf(submitted)));
    LOGGER.info("You can monitor their progress with: {}", Console.bold("./platinum status"));
}
Also used : PipelineServiceAccount(com.hartwig.platinum.iam.PipelineServiceAccount) GcpConfiguration(com.hartwig.platinum.config.GcpConfiguration) TumorNormalPair(com.hartwig.platinum.p5sample.TumorNormalPair) ServiceAccountPrivateKey(com.hartwig.platinum.iam.ServiceAccountPrivateKey) SampleBucket(com.hartwig.platinum.config.SampleBucket) JsonKey(com.hartwig.platinum.iam.JsonKey)

Aggregations

GcpConfiguration (com.hartwig.platinum.config.GcpConfiguration)2 JsonKey (com.hartwig.platinum.iam.JsonKey)2 TumorNormalPair (com.hartwig.platinum.p5sample.TumorNormalPair)2 GoogleJsonResponseException (com.google.api.client.googleapis.json.GoogleJsonResponseException)1 Container (com.google.api.services.container.v1beta1.Container)1 Create (com.google.api.services.container.v1beta1.Container.Projects.Locations.Clusters.Create)1 Get (com.google.api.services.container.v1beta1.Container.Projects.Locations.Clusters.Get)1 Cluster (com.google.api.services.container.v1beta1.model.Cluster)1 CreateClusterRequest (com.google.api.services.container.v1beta1.model.CreateClusterRequest)1 IPAllocationPolicy (com.google.api.services.container.v1beta1.model.IPAllocationPolicy)1 NodeConfig (com.google.api.services.container.v1beta1.model.NodeConfig)1 NodePool (com.google.api.services.container.v1beta1.model.NodePool)1 Operation (com.google.api.services.container.v1beta1.model.Operation)1 PrivateClusterConfig (com.google.api.services.container.v1beta1.model.PrivateClusterConfig)1 Console (com.hartwig.platinum.Console)1 BatchConfiguration (com.hartwig.platinum.config.BatchConfiguration)1 PlatinumConfiguration (com.hartwig.platinum.config.PlatinumConfiguration)1 SampleBucket (com.hartwig.platinum.config.SampleBucket)1 PipelineServiceAccount (com.hartwig.platinum.iam.PipelineServiceAccount)1 ServiceAccountPrivateKey (com.hartwig.platinum.iam.ServiceAccountPrivateKey)1