Java Code Examples for com.google.api.client.util.Strings#isNullOrEmpty()

private static String checkIssuerAudiences(
    ApiIssuerConfigs issuerConfigs, ApiIssuerAudienceConfig issuerAudiences) {
  if (!issuerAudiences.isEmpty()) {
    return null;
  }
  for (Map.Entry<String, Collection<String>> entry : issuerAudiences.asMap().entrySet()) {
    if (!issuerConfigs.hasIssuer(entry.getKey())) {
      return "cannot specify audiences for unknown issuer '" + entry.getKey() + "'";
    }
    for (String audience : entry.getValue()) {
      if (Strings.isNullOrEmpty(audience)) {
        return "issuer '" + entry.getKey() + "' cannot have null or blank audiences";
      }
    }
  }
  return null;
}
 

private String retrieveReferenceBases(Genomics genomics, Annotation annotation) throws IOException {
  StringBuilder b = new StringBuilder();
  String pageToken = "";
  while (true) {
    // TODO: Support full request parameterization for Paginator.References.Bases.
    ListBasesResponse response = genomics.references().bases()
        .list(annotation.getReferenceId())
        .setStart(annotation.getStart())
        .setEnd(annotation.getEnd())
        .setPageToken(pageToken)
        .execute();
    b.append(response.getSequence());
    pageToken = response.getNextPageToken();
    if (Strings.isNullOrEmpty(pageToken)) {
      break;
    }
  }
  return b.toString();
}
 

/**
 * @param builder builder
 *
 * @since 1.14
 */
protected AbstractGoogleClient(Builder builder) {
  googleClientRequestInitializer = builder.googleClientRequestInitializer;
  rootUrl = normalizeRootUrl(builder.rootUrl);
  servicePath = normalizeServicePath(builder.servicePath);
  batchPath = builder.batchPath;
  if (Strings.isNullOrEmpty(builder.applicationName)) {
    logger.warning("Application name is not set. Call Builder#setApplicationName.");
  }
  applicationName = builder.applicationName;
  requestFactory = builder.httpRequestInitializer == null
      ? builder.transport.createRequestFactory()
      : builder.transport.createRequestFactory(builder.httpRequestInitializer);
  objectParser = builder.objectParser;
  suppressPatternChecks = builder.suppressPatternChecks;
  suppressRequiredParameterChecks = builder.suppressRequiredParameterChecks;
}
 

@Override
public Authentication attemptAuthentication(HttpServletRequest request, HttpServletResponse response) {
	final String authToken = request.getHeader(TOKEN_HEADER);
	if (Strings.isNullOrEmpty(authToken)) {
		throw new RuntimeException("Invaild auth token");
	}

	return getAuthenticationManager().authenticate(new FirebaseAuthenticationToken(authToken));
}
 

private static String checkIssuers(ApiIssuerConfigs issuers) {
  if (!issuers.isSpecified()) {
    return null;
  }
  for (IssuerConfig issuer : issuers.asMap().values()) {
    if (Strings.isNullOrEmpty(issuer.getName())) {
      return "issuer name cannot be blank";
    } else if (Strings.isNullOrEmpty(issuer.getIssuer())) {
      return "issuer '" + issuer.getName() + "' cannot have a blank issuer value";
    }
  }
  return null;
}
 

@ProcessElement
public void processElement(DoFn<String, String>.ProcessContext c) throws Exception {
  String readGroupSetId = c.element();
  String referenceSetId = GenomicsUtils.getReferenceSetId(readGroupSetId, auth);
  if (Strings.isNullOrEmpty(referenceSetId)) {
    throw new IllegalArgumentException("No ReferenceSetId associated with ReadGroupSetId "
        + readGroupSetId
        + ". All ReadGroupSets in given input must have an associated ReferenceSet.");
  }
  if (!referenceSetIdForAllReadGroupSets.equals(referenceSetId)) {
    throw new IllegalArgumentException("ReadGroupSets in given input must all be associated with"
        + " the same ReferenceSetId : " + referenceSetId);
  }
  c.output(readGroupSetId);
}
 

/**
 * Run the VerifyBamId algorithm and output the resulting contamination estimate.
 */
public static void main(String[] args) throws GeneralSecurityException, IOException {
  // Register the options so that they show up via --help
  PipelineOptionsFactory.register(Options.class);
  pipelineOptions = PipelineOptionsFactory.fromArgs(args)
      .withValidation().as(Options.class);
  // Option validation is not yet automatic, we make an explicit call here.
  Options.Methods.validateOptions(pipelineOptions);

  // Set up the prototype request and auth.
  StreamVariantsRequest.Builder request = StreamVariantsRequest.newBuilder()
      .setVariantSetId(pipelineOptions.getVariantSetId());
  if (null != pipelineOptions.getProject()) {
    request.setProjectId(pipelineOptions.getProject());
  }
  StreamVariantsRequest prototype = request.build();
  auth = GenomicsOptions.Methods.getGenomicsAuth(pipelineOptions);

  p = Pipeline.create(pipelineOptions);
  registerPipelineCoders(p);

  if (pipelineOptions.getInputDatasetId().isEmpty() && pipelineOptions.getReadGroupSetIds().isEmpty()) {
    throw new IllegalArgumentException("InputDatasetId or ReadGroupSetIds must be specified");
  }

  List<String> rgsIds;
  if (pipelineOptions.getInputDatasetId().isEmpty()) {
    rgsIds = Lists.newArrayList(pipelineOptions.getReadGroupSetIds().split(","));
  } else {
    rgsIds = GenomicsUtils.getReadGroupSetIds(pipelineOptions.getInputDatasetId(), auth);
  }

  // Grab one ReferenceSetId to be used within the pipeline to confirm that all ReadGroupSets
  // are associated with the same ReferenceSet.
  String referenceSetId = GenomicsUtils.getReferenceSetId(rgsIds.get(0), auth);
  if (Strings.isNullOrEmpty(referenceSetId)) {
    throw new IllegalArgumentException("No ReferenceSetId associated with ReadGroupSetId "
        + rgsIds.get(0)
        + ". All ReadGroupSets in given input must have an associated ReferenceSet.");
  }

  // TODO: confirm that variant set also corresponds to the same reference
  // https://github.com/googlegenomics/api-client-java/issues/66

  // Reads in Reads.
  PCollection<Read> reads = p.begin()
      .apply(Create.of(rgsIds))
      .apply(ParDo.of(new CheckMatchingReferenceSet(referenceSetId, auth)))
      .apply(new ReadGroupStreamer(auth, ShardBoundary.Requirement.STRICT, null,
                                   SexChromosomeFilter.INCLUDE_XY));

  /*
  TODO:  We can reduce the number of requests needed to be created by doing the following:
  1. Stream the Variants first (rather than concurrently with the Reads).  Select a subset of
     them equal to some threshold (say 50K by default).
  2. Create the requests for streaming Reads by running a ParDo over the selected Variants
     to get their ranges (we only need to stream Reads that overlap the selected Variants).
  3. Stream the Reads from the created requests.
  */

  // Reads in Variants. TODO potentially provide an option to load the Variants from a file.
  List<StreamVariantsRequest> variantRequests = pipelineOptions.isAllReferences() ?
      ShardUtils.getVariantRequests(prototype, ShardUtils.SexChromosomeFilter.INCLUDE_XY,
          pipelineOptions.getBasesPerShard(), auth) :
      ShardUtils.getVariantRequests(prototype, pipelineOptions.getBasesPerShard(), pipelineOptions.getReferences());

  PCollection<Variant> variants = p.apply(Create.of(variantRequests))
      .apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS));

  PCollection<KV<Position, AlleleFreq>> refFreq = getFreq(variants, pipelineOptions.getMinFrequency());

  PCollection<KV<Position, ReadCounts>> readCountsTable =
      combineReads(reads, pipelineOptions.getSamplingFraction(), HASH_PREFIX, refFreq);

  // Converts our results to a single Map of Position keys to ReadCounts values.
  PCollectionView<Map<Position, ReadCounts>> view = readCountsTable
      .apply(View.<Position, ReadCounts>asMap());

  // Calculates the contamination estimate based on the resulting Map above.
  PCollection<String> result = p.begin()
      .apply(Create.of(""))
      .apply(ParDo.of(new Maximizer(view)).withSideInputs(view));

  // Writes the result to the given output location in Cloud Storage.
  result.apply("WriteOutput", TextIO.write().to(pipelineOptions.getOutput()).withoutSharding());

  p.run();
}
 

public static void main(String[] args) throws GeneralSecurityException, IOException, URISyntaxException {
  // Register the options so that they show up via --help
  PipelineOptionsFactory.register(Options.class);
  options = PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class);

  auth = GenomicsOptions.Methods.getGenomicsAuth(options);

  p = Pipeline.create(options);
  registerPipelineCoders(p);

  if (options.getBamInput().isEmpty() && options.getInputDatasetId().isEmpty() && options.getReadGroupSetIds().isEmpty()) {
    throw new IllegalArgumentException("BamInput or InputDatasetId or ReadGroupSetIds must be specified");
  }

  PCollection<Read> reads = null;
  String referenceSetId = options.getReferenceSetId();

  if (!options.getBamInput().isEmpty()) {

    if (options.isAllReferences()) {
      throw new IllegalArgumentException("--allReferences is not currently supported for BAM "
      + "file reading. Instead use --references and list all of the genomic regions in the file.");
    }

    final List<Contig> contigs = Lists.newArrayList(Contig.parseContigsFromCommandLine(options.getReferences()));
    final ReaderOptions readerOptions = new ReaderOptions(
        ValidationStringency.LENIENT,
        false);  // Do not include unmapped reads.

    ShardingPolicy policy = new ShardingPolicy() {
      final int MAX_BYTES_PER_SHARD = options.getMaxShardSizeBytes();
      @Override
      public Boolean apply(BAMShard shard) {
        return shard.approximateSizeInBytes() > MAX_BYTES_PER_SHARD;
      }
    };

    reads = ReadBAMTransform.getReadsFromBAMFilesSharded (
        p,
        options,
        auth,
        contigs,
        readerOptions,
        options.getBamInput(),
        policy);

  } else {

    List<String> rgsIds;
    if (options.getInputDatasetId().isEmpty()) {
      rgsIds = Lists.newArrayList(options.getReadGroupSetIds().split(","));
    } else {
      rgsIds = GenomicsUtils.getReadGroupSetIds(options.getInputDatasetId(), auth);
    }

    if (rgsIds.size() < options.getNumQuantiles()) {
      throw new IllegalArgumentException("Number of ReadGroupSets must be greater than or equal to"
          + " the number of requested quantiles.");
    }

    // Grab one ReferenceSetId to be used within the pipeline to confirm that all ReadGroupSets
    // are associated with the same ReferenceSet.
    referenceSetId = GenomicsUtils.getReferenceSetId(rgsIds.get(0), auth);
    if (Strings.isNullOrEmpty(referenceSetId)) {
      throw new IllegalArgumentException("No ReferenceSetId associated with ReadGroupSetId "
          + rgsIds.get(0)
          + ". All ReadGroupSets in given input must have an associated ReferenceSet.");
    }

    reads = p.begin()
        .apply(Create.of(rgsIds))
        .apply(ParDo.of(new CheckMatchingReferenceSet(referenceSetId, auth)))
        .apply(new ReadGroupStreamer(auth, ShardBoundary.Requirement.STRICT, READ_FIELDS, SexChromosomeFilter.INCLUDE_XY));
  }

  // Create our destination AnnotationSet for the associated ReferenceSet.
  AnnotationSet annotationSet = createAnnotationSet(referenceSetId);

  PCollection<KV<PosRgsMq, Double>> coverageMeans = reads.apply("CalculateCoverateMean",
      new CalculateCoverageMean(options.getBucketWidth()));
  PCollection<KV<Position, KV<PosRgsMq.MappingQuality, List<Double>>>> quantiles
      = coverageMeans.apply("CalculateQuantiles", new CalculateQuantiles(options.getNumQuantiles()));
  PCollection<KV<Position, Iterable<KV<PosRgsMq.MappingQuality, List<Double>>>>> answer =
      quantiles.apply(GroupByKey.<Position, KV<PosRgsMq.MappingQuality, List<Double>>>create());
  answer.apply("CreateAnnotations", ParDo.of(new CreateAnnotations(annotationSet.getId(), auth, true)));

  p.run();
}