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

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

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    // Readset summary
    Mockito.when(readsets.search(new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList("id1")).setPageSize(100)))
        .thenReturn(readsetSearch);
    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse()
        .setReadGroupSets(Lists.newArrayList(new ReadGroupSet(), new ReadGroupSet())));

    // Variant set
    Mockito.when(variantSets.get("id1")).thenReturn(variantSetGet);
    Mockito.when(variantSetGet.execute()).thenReturn(new VariantSet().setReferenceBounds(
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        .thenThrow(GoogleJsonResponseException.class);

    // Readset summary
    Mockito.when(readsets.search(Mockito.any(SearchReadGroupSetsRequest.class)))
        .thenReturn(readsetSearch);
    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse());

    // Variant set
    Mockito.when(variantSets.get(Mockito.anyString())).thenReturn(variantSetGet);
    Mockito.when(variantSetGet.execute()).thenReturn(new VariantSet());
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    Mockito.when(readsets.search(new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList("dataset"))
        .setName("12878")
        .setPageSize(10)))
        .thenReturn(readsetSearch);
    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse()
        .setReadGroupSets(Lists.<ReadGroupSet>newArrayList()));

    command.handleRequest(genomics);

    String output = outContent.toString();
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  private String getReadsetCount(Genomics genomics, String datasetId) throws IOException {
    SearchReadGroupSetsRequest readsetSearch = new SearchReadGroupSetsRequest()
        .setDatasetIds(com.google.common.collect.Lists.newArrayList(datasetId))
        .setPageSize(100);

    SearchReadGroupSetsResponse readGroupSets = genomics.readgroupsets()
        .search(readsetSearch).setFields("nextPageToken,readGroupSets(id)").execute();
    if (readGroupSets.getReadGroupSets() == null) {
      return "0";
    }

    if (Strings.isNullOrEmpty(readGroupSets.getNextPageToken())) {
      return String.valueOf(readGroupSets.getReadGroupSets().size());
    } else {
      return "More than 100";
    }
  }
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Related Classes of com.google.api.services.genomics.model.SearchReadGroupSetsResponse

  • com.google.cloud.genomics.api.client.commands.BaseCommand
  • com.google.cloud.genomics.api.client.commands.ListDatasetsCommandTest
  • com.google.cloud.genomics.api.client.commands.SearchReadGroupSetsCommandTest
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