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

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

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    command.bamFiles = Lists.newArrayList("uri1");
    command.datasetId = "abc";

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

    Mockito.when(readsets.call(new CallReadGroupSetsRequest()
        .setDatasetId("abc").setSourceUris(Lists.newArrayList("uri1"))))
        .thenReturn(readsetCall);
    Mockito.when(readsetCall.execute()).thenReturn(
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    command.datasetId = "abc";

    // Get the dataset
    Mockito.when(datasets.get("abc")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(
        new Dataset().setId("abc").setName("1kg"));

    // Import them
    Mockito.when(readsets.align(Mockito.any(AlignReadGroupSetsRequest.class)))
        .thenReturn(readsetAlign);
    Mockito.when(readsetAlign.execute()).thenReturn(
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    command.referenceName = "chr1";
    command.start = 1L;
    command.end = 5L;

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

    Mockito.when(variants.search(Mockito.any(SearchVariantsRequest.class)))
        .thenReturn(variantSearch);
    Mockito.when(variantSearch.execute()).thenReturn(new SearchVariantsResponse()
        .setVariants(Lists.<Variant>newArrayList()));
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    command.start = 1L;
    command.end = 5L;
    command.callSetNames = Lists.newArrayList("c1", "c2");

    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("c1")))
        .thenReturn(callsetSearch);
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    command.datasetId = "abc";

    // Get the dataset
    Mockito.when(datasets.get("abc")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(
        new Dataset().setId("abc").setName("1kg"));

    // Import them
    Mockito.when(readsets.align(new AlignReadGroupSetsRequest()
        .setDatasetId("abc").setBamSourceUris(Lists.newArrayList("uri1"))))
        .thenReturn(readsetAlign);
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    command.datasetId = "abc";

    // Get the dataset
    Mockito.when(datasets.get("abc")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(
        new Dataset().setId("abc").setName("1kg"));

    // Import them
    Mockito.when(readsets.align(Mockito.any(AlignReadGroupSetsRequest.class)))
        .thenReturn(readsetAlign);
    Mockito.when(readsetAlign.execute()).thenReturn(
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  @Test
  public void testListDatasets_withoutDetails() throws Exception {
    ListDatasetsCommand command = new ListDatasetsCommand();
    command.setDataStoreFactory(new MemoryDataStoreFactory());

    command.addDatasetToHistory(new Dataset().setName("name").setId("id"));
    command.handleRequest(null /* should be unused */);

    String output = outContent.toString();
    assertTrue(output, output.contains("name (ID: id)"));
  }
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    Mockito.when(datasets.list()).thenReturn(datasetList);
    Mockito.when(datasetList.setProjectNumber(10L)).thenReturn(datasetList);
    Mockito.when(datasetList.execute()).thenReturn(new ListDatasetsResponse()
        .setDatasets(Lists.newArrayList(
            new Dataset().setId("id1").setName("name").setProjectNumber(1234L))));

    // Readset summary
    Mockito.when(readsets.search(new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList("id1")).setPageSize(100)))
        .thenReturn(readsetSearch);
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  @Test
  public void testListDatasets_withDeletedData() throws Exception {
    ListDatasetsCommand command = new ListDatasetsCommand();
    command.setDataStoreFactory(new MemoryDataStoreFactory());

    Dataset dataset = new Dataset().setName("name1").setId("id");
    command.addDatasetToHistory(dataset);
    command.addDatasetToHistory(new Dataset().setName("name2").setId("deleted"));
    command.includeDetails = true;


    Mockito.when(datasets.get(Mockito.anyString())).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute())
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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(readsets.search(new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList("dataset"))
        .setName("12878")
        .setPageSize(10)))
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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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