Examples with HmfApi com.hartwig.api.HmfApi used on opensource projects

Example 1 with HmfApi

use of com.hartwig.api.HmfApi in project platinum by hartwigmedical.

the class PlatinumMain method call.

@Override
public Integer call() {
    try {
        PlatinumConfiguration configuration = addRegionAndProject(PlatinumConfiguration.from(inputJson));
        Validation.apply(runName, configuration);
        final HmfApi api = HmfApi.create(HmfApi.PRODUCTION);
        new Platinum(runName, inputJson, StorageOptions.newBuilder().setProjectId(configuration.gcp().projectOrThrow()).build().getService(), IamProvider.get(), ResourceManagerProvider.get(), new KubernetesEngine(ContainerProvider.get(), new ProcessRunner(), configuration), configuration, new ApiRerun(api.runs(), api.sets(), api.samples(), configuration.outputBucket().get(), "5.28.2")).run();
        return 0;
    } catch (Exception e) {
        LOGGER.error("Unexpected exception", e);
        return 1;
    }
}

Example 2 with HmfApi

use of com.hartwig.api.HmfApi in project pipeline5 by hartwigmedical.

the class SomaticMetadataApiProvider method diagnosticRun.

public SomaticMetadataApi diagnosticRun(final Integer setId) {
    HmfApi api = HmfApi.create(arguments.sbpApiUrl());
    Run run = api.runs().get((long) arguments.sbpApiRunId().orElseThrow());
    return new DiagnosticSomaticMetadataApi(run, api.runs(), api.samples(), createPublisher(SetResolver.forApi(api.sets()), Optional.of(run), arguments.context(), false), new Anonymizer(arguments));
}

Example 3 with HmfApi

use of com.hartwig.api.HmfApi in project pipeline5 by hartwigmedical.

the class SomaticMetadataApiProvider method researchRun.

public SomaticMetadataApi researchRun(final String biopsyName) {
    HmfApi api = HmfApi.create(arguments.sbpApiUrl());
    Optional<Run> run = arguments.sbpApiRunId().map(id -> api.runs().get((long) id));
    return new ResearchMetadataApi(api.samples(), api.sets(), api.runs(), run, biopsyName, arguments, createPublisher(SetResolver.forApi(api.sets()), run.or(() -> Optional.of(new Run().id(0L))), Context.RESEARCH, true), new Anonymizer(arguments));
}