Package com.google.api.services.genomics.model

Examples of com.google.api.services.genomics.model.Dataset

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    // Validate the datasetId
    if (getDataset(genomics, datasetId) == null) {
      return;
    }

    Dataset dataset = new Dataset().setId(datasetId);
    if (name != null) {
      dataset.setName(name);
    }
    if (isPublic != null) {
      dataset.setIsPublic(isPublic);
    }
    dataset = genomics.datasets().patch(datasetId, dataset).execute();

    addDatasetToHistory(dataset);
    System.out.println("The dataset was updated: " + dataset.toPrettyString());
  }
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  }

  protected Dataset getDataset(Genomics genomics, String datasetId, boolean handleException)
      throws IOException {
    try {
      Dataset dataset = genomics.datasets().get(datasetId).execute();
      addDatasetToHistory(dataset);
      return dataset;
    } catch (GoogleJsonResponseException e) {
      if (!handleException) {
        throw e;
      }

      String message = e.getDetails() == null ? "unknown failure" : e.getDetails().getMessage();
      System.out.println("That datasetId won't work: " + message + "\n");

      Map<String, String> previousDatasets = getPreviousDatasets();
      if (previousDatasets.isEmpty()) {
        System.out.println("There aren't any recently used datasets, " +
            "if you want to make a new one try the 'createdataset' command.");
        System.out.println("You can also try the public 1000 Genomes dataset ID: 10473108253681171589");

      } else {
        System.out.println("In the past, you've used these datasets: ");
        for (Map.Entry<String, String> dataset : previousDatasets.entrySet()) {
          System.out.println(dataset.getKey() + ": " + dataset.getValue());
        }
      }

      // TODO: This call won't do what we want right now
      // ListDatasetsResponse allDatasets = genomics.datasets().list().execute();
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  public String name;

  @Override
  public void handleRequest(Genomics genomics) throws IOException {

    Dataset dataset = getDataset(genomics, datasetId);
    if (dataset == null) {
      return;
    }
    System.out.println("Getting call sets from: " + dataset.getName());

    SearchCallSetsRequest request = new SearchCallSetsRequest()
        .setVariantSetIds(Lists.newArrayList(datasetId))
        .setName(name)
        .setPageSize(getMaxResults());
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  public String name;

  @Override
  public void handleRequest(Genomics genomics) throws IOException {

    Dataset dataset = getDataset(genomics, datasetId);
    if (dataset == null) {
      return;
    }
    System.out.println("Getting read group sets from: " + dataset.getName());

    SearchReadGroupSetsRequest request = new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList(datasetId))
        .setName(name)
        .setPageSize(getMaxResults());
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      System.out.println("You can not provide both --read_group_set_id and --bam_file.");
      return;
    }

    // Validate the dataset
    Dataset dataset = getDataset(genomics, datasetId);
    if (dataset == null) {
      return;
    }
    System.out.println("Saving called variants into: " + dataset.getName());

    // Start the job
    Genomics.Readgroupsets.Call req = genomics.readgroupsets().call(
        new CallReadGroupSetsRequest()
            .setDatasetId(datasetId)
            .setReadGroupSetIds(readGroupSetIds)
            .setSourceUris(bamFiles));
    String jobId = req.execute().getJobId();

    // Get the resulting job
    addJobToHistory(jobId, "Saving called variants into " + dataset.getName() + " from "
        + Joiner.on(',').join(bamFiles == null ? readGroupSetIds : bamFiles));
    Job job = getJob(genomics, jobId, pollForStatus);
    System.out.println("Variant calling job: ");
    printJob(job);
  }
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  protected abstract List<String> getSources();

  @Override
  public void handleRequest(Genomics genomics) throws IOException {
    // Validate the dataset
    Dataset dataset = getDataset(genomics, datasetId);
    if (dataset == null) {
      return;
    }
    System.out.println("Putting aligned read group sets into: " + dataset.getName());

    Genomics.Readgroupsets.Align req = genomics.readgroupsets()
        .align(getRequest().setDatasetId(datasetId));
    String jobId = req.execute().getJobId();

    // Get the resulting job
    addJobToHistory(jobId, "Aligning read group sets to " + dataset.getName() + " from "
        + Joiner.on(',').join(getSources()));
    Job job = getJob(genomics, jobId, pollForStatus);
    System.out.println("Aligning job: ");
    printJob(job);
  }
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Related Classes of com.google.api.services.genomics.model.Dataset

  • com.google.cloud.genomics.api.client.commands.align.AlignBamsCommandTest
  • com.google.cloud.genomics.api.client.commands.align.AlignInterleavedFastqsCommandTest
  • com.google.cloud.genomics.api.client.commands.align.AlignPairedFastqsCommandTest
  • com.google.cloud.genomics.api.client.commands.align.BaseAlignCommand
  • com.google.cloud.genomics.api.client.commands.BaseCommand
  • com.google.cloud.genomics.api.client.commands.BaseCommandTest
  • com.google.cloud.genomics.api.client.commands.CallVariantsCommand
  • com.google.cloud.genomics.api.client.commands.CallVariantsCommandTest
  • com.google.cloud.genomics.api.client.commands.CreateDatasetCommand
  • com.google.cloud.genomics.api.client.commands.CreateDatasetCommandTest
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