org.opencb.opencga.core.results.VariantQueryResult.getSource()方法的使用及代码示例

x33g5p2x  于2022-02-01 转载在 其他  
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本文整理了Java中org.opencb.opencga.core.results.VariantQueryResult.getSource()方法的一些代码示例，展示了VariantQueryResult.getSource()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。VariantQueryResult.getSource()方法的具体详情如下：
包路径：org.opencb.opencga.core.results.VariantQueryResult
类名称：VariantQueryResult
方法名：getSource

VariantQueryResult.getSource介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

@Test
public void testSummary() {
  queryResult = query(new Query(), new QueryOptions(VariantField.SUMMARY, true).append(QueryOptions.LIMIT, 1000));
  System.out.println("queryResult = " + ((VariantQueryResult) queryResult).getSource());
  assertEquals(allVariants.getResult().size(), queryResult.getResult().size());
  for (Variant variant : queryResult.getResult()) {
    assertThat(variant.getStudies().get(0).getSamplesData(), is(Collections.emptyList()));
    assertThat(variant.getStudies().get(0).getFiles(), is(Collections.emptyList()));
  }
}

代码示例来源：origin: opencb/opencga

@SuppressWarnings("unchecked")
public <T> VariantQueryResult<T> get(Query query, QueryOptions queryOptions, String sessionId, Class<T> clazz)
    throws CatalogException, IOException, StorageEngineException {
  VariantQueryResult<Variant> result = get(query, queryOptions, sessionId);
  List<T> variants;
  if (clazz == Variant.class) {
    return (VariantQueryResult<T>) result;
  } else if (clazz == org.ga4gh.models.Variant.class) {
    Ga4ghVariantConverter<org.ga4gh.models.Variant> converter = new Ga4ghVariantConverter<>(new AvroGa4GhVariantFactory());
    variants = (List<T>) converter.apply(result.getResult());
  } else if (clazz == ga4gh.Variants.Variant.class) {
    Ga4ghVariantConverter<ga4gh.Variants.Variant> converter = new Ga4ghVariantConverter<>(new ProtoGa4GhVariantFactory());
    variants = (List<T>) converter.apply(result.getResult());
  } else {
    throw new IllegalArgumentException("Unknown variant format " + clazz);
  }
  return new VariantQueryResult<>(
      result.getId(),
      result.getDbTime(),
      result.getNumResults(),
      result.getNumTotalResults(),
      result.getWarningMsg(),
      result.getErrorMsg(),
      variants,
      result.getSamples(),
      result.getSource(),
      result.getApproximateCount(),
      result.getApproximateCountSamplingSize());
}

代码示例来源：origin: opencb/opencga

public void testGetBySampleName(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
        .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.SAMPLE.key(), "NA12877");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options);
    assertEquals(expectedSource, queryResult.getSource());
    assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", containsString("1"))))));
  }

代码示例来源：origin: opencb/opencga

public void testGetBySamplesName(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
        .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.SAMPLE.key(), "NA12877;NA12878");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"), options);
    assertEquals(expectedSource, queryResult.getSource());
    assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
        allOf(
            withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"),
            withSampleData("NA12877", "GT", containsString("1"))),
        allOf(
            withFileId("1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"),
            withSampleData("NA12878", "GT", containsString("1")))))));
  }

代码示例来源：origin: opencb/opencga

public void testGetByGenotypes(String expectedSource, QueryOptions options) throws Exception {
  VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
      .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
      .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878")
      .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"), options);
  queryResult = variantStorageEngine.get(new Query()
      .append(VariantQueryParam.STUDY.key(), "S_1")
      .append(VariantQueryParam.GENOTYPE.key(), "NA12877:0/1,NA12878:1/1")
      .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878"), options);
  assertThat(queryResult, everyResult(allVariants, withStudy("S_1", anyOf(
      allOf(
          withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"),
          withSampleData("NA12877", "GT", containsString("0/1"))),
      allOf(
          withFileId("1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"),
          withSampleData("NA12878", "GT", containsString("1/1")))))));
  assertEquals(expectedSource, queryResult.getSource());
  queryResult = variantStorageEngine.get(new Query()
      .append(VariantQueryParam.STUDY.key(), "S_1")
      .append(VariantQueryParam.GENOTYPE.key(), "NA12877:" + GenotypeClass.HET_REF + ",NA12878:" + GenotypeClass.HOM_ALT)
      .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878"), options);
  assertThat(queryResult, everyResult(allVariants, withStudy("S_1", anyOf(
      allOf(
          withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"),
          withSampleData("NA12877", "GT", containsString("0/1"))),
      allOf(
          withFileId("1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz"),
          withSampleData("NA12878", "GT", containsString("1/1")))))));
  assertEquals(expectedSource, queryResult.getSource());
}

代码示例来源：origin: opencb/opencga

public void testGetByFileName(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
//                .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "all")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options);
    assertEquals(expectedSource, queryResult.getSource());
    assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"))));
  }

代码示例来源：origin: opencb/opencga

public void testGetByGenotypesWithRefMix(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
        .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.GENOTYPE.key(), "NA12877:0/1;NA12878:0/0,0/1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878")
        .append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "0/0");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz")
        .append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "0/0"), options);
    assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
        allOf(
            withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"),
            withSampleData("NA12877", "GT", containsString("0/1"))),
        anyOf(
            withSampleData("NA12878", "GT", containsString("0/0")),
            withSampleData("NA12878", "GT", containsString("0/1"))
        )
    ))));
    assertEquals(expectedSource, queryResult.getSource());
  }

代码示例来源：origin: opencb/opencga

public void testGetByGenotypesWithRef(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
        .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.GENOTYPE.key(), "NA12877:0/1;NA12878:0/0")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878")
        .append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "0/0");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877,NA12878")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz,1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz")
        .append(VariantQueryParam.UNKNOWN_GENOTYPE.key(), "0/0"), options);
    assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
        allOf(
            withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"),
            withSampleData("NA12877", "GT", containsString("0/1"))),
        withSampleData("NA12878", "GT", containsString("0/0"))))));
    assertEquals(expectedSource, queryResult.getSource());
  }

代码示例来源：origin: opencb/opencga

public void testGetBySampleNameMultiRegion(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
        .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.SAMPLE.key(), "NA12877")
        .append(VariantQueryParam.REGION.key(), "1:1-12783,M");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options);
    assertEquals(expectedSource, queryResult.getSource());
    assertThat(queryResult, everyResult(allVariants, allOf(anyOf(overlaps(new Region("1:1-12783")), overlaps(new Region("M"))), withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", containsString("1")))))));
  }

代码示例来源：origin: opencb/opencga

public void testGetByGenotypeMultiRegion(String expectedSource, QueryOptions options) throws Exception {
    query = new Query()
        .append(VariantQueryParam.STUDY.key(), "S_1")
        .append(VariantQueryParam.GENOTYPE.key(), "NA12877:1/1")
        .append(VariantQueryParam.REGION.key(), "1:1-12783,M");
//        queryResult = dbAdaptor.get(query, options);
    queryResult = variantStorageEngine.get(query, options);
    VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
        .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
        .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877")
        .append(VariantQueryParam.INCLUDE_FILE.key(), "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), options);
    assertEquals(expectedSource, queryResult.getSource());
    assertThat(queryResult, everyResult(allVariants, allOf(anyOf(overlaps(new Region("1:1-12783")), overlaps(new Region("M"))), withStudy("S_1", allOf(withFileId("1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz"), withSampleData("NA12877", "GT", is("1/1")))))));
  }

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