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

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

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    command.datasetId = "dataset";
    command.name = "12878";

    Mockito.when(datasets.get("dataset")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(new Dataset().setId("id").setName("1kg"));

    Mockito.when(callsets.search(new SearchCallSetsRequest()
        .setVariantSetIds(Lists.newArrayList("dataset"))
        .setName("12878")
        .setPageSize(10)))
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    command.setDataStoreFactory(new MemoryDataStoreFactory());

    command.projectNumber = 5L;
    command.name = "dataset";

    Dataset expectedDataset = new Dataset().setName("dataset")
        .setProjectNumber(5L).setIsPublic(false);

    Mockito.when(datasets.create(expectedDataset)).thenReturn(datasetCreate);
    Mockito.when(datasetCreate.execute()).thenReturn(expectedDataset.clone().setId("id"));

    command.handleRequest(genomics);

    Map<String,String> previousDatasets = command.getPreviousDatasets();
    assertEquals(1, previousDatasets.size());
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  @Test
  public void testDatasetHistory() throws Exception {
    assertTrue(command.getPreviousDatasets().isEmpty());

    Dataset dataset = new Dataset();
    dataset.setId("d1");
    dataset.setName("name1");
    command.addDatasetToHistory(dataset);

    Map<String,String> datasets = command.getPreviousDatasets();
    assertEquals(1, datasets.size());
    assertEquals("name1", datasets.get("d1"));
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    Assert.assertTrue(output, output.contains("1000 Genomes dataset ID"));
  }

  @Test
  public void testGetBadDataset_withHistory() throws Exception {
    Dataset dataset = new Dataset();
    dataset.setId("d1");
    dataset.setName("name1");
    command.addDatasetToHistory(dataset);

    Mockito.when(datasets.get("d2")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenThrow(GoogleJsonResponseException.class);
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    command.setDataStoreFactory(new MemoryDataStoreFactory());

    command.datasetIds = Lists.newArrayList("d1", "d2");
    command.includeDetails = false;

    Dataset dataset1 = new Dataset().setId("d1").setName("name1");
    Dataset dataset2 = new Dataset().setId("d2").setName("name2");

    Mockito.when(datasets.get("d1")).thenReturn(datasetGet);
    Mockito.when(datasets.get("d2")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(dataset1, dataset2);
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    command.datasetId = "id";
    command.name = "name";

    Mockito.when(datasets.get("id")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(new Dataset().setId("id").setName("old"));

    Dataset expectedDataset = new Dataset().setId("id").setName("name");
    Mockito.when(datasets.patch("id", expectedDataset)).thenReturn(datasetPatch);
    Mockito.when(datasetPatch.execute()).thenReturn(expectedDataset);

    command.handleRequest(genomics);
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  }

  @Override
  public void handleRequest(Genomics genomics) throws IOException {
    // Validate the dataset
    Dataset dataset = getDataset(genomics, variantSetId);
    if (dataset == null) {
      return;
    }

    System.out.println("Exporting variants for variant set " + dataset.getName());
    if (callSetIds != null && !callSetIds.isEmpty()) {
      System.out.println(Joiner.on(',').join(callSetIds));
    }

    // Start the export
    ExportVariantSetRequest request = new ExportVariantSetRequest()
        .setProjectNumber(projectNumber)
        .setCallSetIds(callSetIds)
        .setBigqueryDataset(bigqueryDataset)
        .setBigqueryTable(bigqueryTable);
    String jobId = genomics.variantsets().export(variantSetId, request).execute().getJobId();

    // Get the resulting job
    addJobToHistory(jobId, "Exporting variants: from " + dataset.getName() +
        " to " + bigqueryDataset + "." + bigqueryTable);
    System.out.println("Export job: ");
    printJob(getJob(genomics, jobId, pollForStatus));
  }
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      description = "Whether the new dataset should be public (by default the dataset is private)")
  public boolean isPublic = false;

  @Override
  public void handleRequest(Genomics genomics) throws IOException {
    Dataset dataset = new Dataset().setName(name)
        .setProjectNumber(projectNumber).setIsPublic(isPublic);
    dataset = genomics.datasets().create(dataset).execute();

    addDatasetToHistory(dataset);
    System.out.println("The new dataset was created: " + dataset.toPrettyString());
  }
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  @Override
  public void handleRequest(Genomics genomics) throws IOException {
    // TODO: Validate the GCS files first?

    // Validate the dataset
    Dataset dataset = getDataset(genomics, datasetId);
    if (dataset == null) {
      return;
    }
    System.out.println("Importing read group sets into: " + dataset.getName());

    // Start the import
    Genomics.Readgroupsets.GenomicsImport req = genomics.readgroupsets().genomicsImport(
        new ImportReadGroupSetsRequest().setDatasetId(datasetId)
            .setSourceUris(bamFiles));
    String jobId = req.execute().getJobId();

    // Get the resulting job
    addJobToHistory(jobId, "Import read group sets to " + dataset.getName() + " from "
        + Joiner.on(',').join(bamFiles));
    Job job = getJob(genomics, jobId, pollForStatus);
    System.out.println("Import job: ");
    printJob(job);
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  public boolean includeDetails = true;

  @Override
  public void handleRequest(Genomics genomics) throws IOException {
    for (String datasetId : datasetIds) {
      Dataset dataset = getDataset(genomics, datasetId);
      if (dataset != null) {
        printDataset(genomics, dataset, includeDetails);
      }
    }
  }
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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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