org.opencb.opencga.core.results.VariantQueryResult.getNumResults()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.getNumResults()方法的一些代码示例，展示了VariantQueryResult.getNumResults()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.getNumResults()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：getNumResults

VariantQueryResult.getNumResults介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

public VariantQueryResult<Variant> get(Query query, QueryOptions queryOptions, String sessionId)
    throws CatalogException, StorageEngineException, IOException {
  return secure(query, queryOptions, sessionId, engine -> {
    addDefaultLimit(queryOptions);
    logger.debug("getVariants {}, {}", query, queryOptions);
    VariantQueryResult<Variant> result = engine.get(query, queryOptions);
    logger.debug("gotVariants {}, {}, in {}ms", result.getNumResults(), result.getNumTotalResults(), result.getDbTime());
    return result;
  });
}

代码示例来源：origin: opencb/opencga

int sampling = variants.getCount();
int limit = options.getInt(QueryOptions.LIMIT, 0);
if (limit > 0 && limit > result.getNumResults()) {
  result.setNumTotalResults(result.getNumResults());
} else if (variants.hasNext()) {
  long totalCount;
    totalCount = variants.getCount();
  long approxCount = totalCount / sampling * result.getNumResults();
  logger.info("totalCount = " + totalCount);
  logger.info("sampling = " + sampling);
  logger.info("result.getNumResults() = " + result.getNumResults());
  logger.info("approxCount = " + approxCount);
  result.setApproximateCount(true);
  logger.info("Genotype index Iterator exhausted");
  logger.info("sampling = " + sampling);
  result.setApproximateCount(sampling != result.getNumResults());
  result.setNumTotalResults(sampling);

代码示例来源：origin: opencb/opencga

private void skipLimit(Query query, QueryOptions options, int batchSize, boolean serverSideSkip) throws StorageEngineException, SolrServerException, IOException {
  Set<String> expectedResults = dbAdaptor.get(query, null).getResult().stream().map(Variant::toString).collect(Collectors.toSet());
  Set<String> results = new HashSet<>();
  int numQueries = (int) Math.ceil(expectedResults.size() / (float) batchSize);
  for (int i = 0; i < numQueries; i++) {
    QueryOptions thisOptions = new QueryOptions(options)
        .append(QueryOptions.SKIP, i * batchSize)
        .append(QueryOptions.LIMIT, batchSize);
    VariantQueryResult<Variant> result = variantStorageEngine.get(query, thisOptions);
    for (Variant variant : result.getResult()) {
      assertTrue(results.add(variant.toString()));
    }
    assertNotEquals(0, result.getNumResults());
  }
  assertEquals(expectedResults, results);
  if (serverSideSkip) {
    long count = mockingDetails(solrClient).getInvocations()
        .stream()
        .filter(invocation -> invocation.getMethod().getName().equals("query"))
        .count();
    System.out.println(SolrClient.class.getName() + ".query(...) invocations : " + count);
    verify(solrClient, atLeast(numQueries)).query(anyString(), any());
  } else {
    verify(solrClient, times(numQueries)).query(anyString(), any());
  }
}

代码示例来源：origin: opencb/opencga

public void limitSkip(Query query, QueryOptions options) {
    VariantQueryResult<Variant> expected = query(query, options);
    int numVariants = expected.getNumResults();
//        expected.getResult().forEach(v -> logger.info("expected variant: == " + v));
    for (int batchSize : new int[]{50, 100, 1000}) {
      List<Variant> variants = new ArrayList<>();
      Set<String> variantStr = new HashSet<>();
      for (int i = 0; i < numVariants / batchSize + 1; i++) {
        QueryResult<Variant> result = query(query, new QueryOptions(options)
            .append(QueryOptions.LIMIT, batchSize)
            .append(QueryOptions.SKIP, i * batchSize));
        logger.info("Got " + result.getNumResults() + " results");
        variants.addAll(result.getResult());
        for (Variant variant : result.getResult()) {
          boolean repeated = !variantStr.add(variant.toString());
          assertFalse("Repeated variant! : " + variant.toString(), repeated);
        }
      }
      assertEquals(numVariants, variants.size());
      assertEquals(numVariants, variantStr.size());
      assertEquals(expected.getResult().stream().map(Object::toString).collect(Collectors.toSet()), variantStr);
    }
  }

代码示例来源：origin: opencb/opencga

System.out.println("extra = " + extra);
assertEquals(message, variants.size(), result.getNumResults());
for (Variant variant : result.getResult()) {
  assertEquals(message, gt, variant.getStudies().get(0).getSampleData(0).get(0));

代码示例来源：origin: opencb/opencga

@Test
public void testIncludeStudies() throws Exception {
  query = new Query()
      .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1");
  this.queryResult = query(query, options);
  assertEquals(dbAdaptor.count(null).first().intValue(), this.queryResult.getNumResults());
  assertThat(this.queryResult, everyResult(allOf(withStudy("S_2", nullValue()), withStudy("S_3", nullValue()), withStudy("S_4", nullValue()))));
}

代码示例来源：origin: opencb/opencga

@Test
public void testIncludeStudiesNone() throws Exception {
  query = new Query(VariantQueryParam.INCLUDE_STUDY.key(), NONE);
  queryResult = query(query, options);
  assertEquals(dbAdaptor.count(null).first().intValue(), queryResult.getNumResults());
  assertThat(queryResult, everyResult(firstStudy(nullValue())));
}

代码示例来源：origin: opencb/opencga

if (variantVariantQueryResult.getNumResults() == 0) {
  variantQuery = new Query();
  query.put(VariantQueryParam.GENE.key(), StringUtils.join(geneIds, ","));

代码示例来源：origin: opencb/opencga

@Test
public void testGetByNegatedFilter() {
  VariantQueryResult<Variant> allVariants = dbAdaptor.get(new Query()
      .append(VariantQueryParam.INCLUDE_SAMPLE.key(), "NA12877")
      .append(VariantQueryParam.INCLUDE_FILE.key(), file12877), options);
  query = new Query()
      .append(VariantQueryParam.FILTER.key(), "LowGQX" + AND + "LowMQ" + AND + NOT + "SiteConflict")
      .append(VariantQueryParam.FILE.key(), file12877);
  queryResult = query(query, options);
  System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
  assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
      with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), allOf(
          containsString("LowGQX"),
          containsString("LowMQ"),
          not(containsString("SiteConflict"))
      ))))));
  query = new Query()
      .append(VariantQueryParam.FILTER.key(), "LowGQX" + AND + "LowQD" + AND + NOT + "\"LowGQX;LowQD;SiteConflict\"")
      .append(VariantQueryParam.FILE.key(), file12877);
  queryResult = query(query, options);
  System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
  assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
      with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), allOf(
          containsString("LowGQX"),
          containsString("LowQD"),
          not(is("LowGQX;LowQD;SiteConflict"))
      ))))));
}

代码示例来源：origin: opencb/opencga

System.out.println("get             = " + allVariants.getNumResults());

代码示例来源：origin: opencb/opencga

@Test
public void testExactApproxCount() throws Exception {
  Query query = new Query(SAMPLE.key(), "NA19660")
      .append(ANNOT_CONSERVATION.key(), "gerp>0.1");
  long realCount = dbAdaptor.count(query).first();
  VariantQueryResult<Long> result = variantStorageEngine
      .approximateCount(query, new QueryOptions(VariantStorageEngine.Options.APPROXIMATE_COUNT_SAMPLING_SIZE.key(), allVariants.getNumResults()));
  long approxCount = result.first();
  System.out.println("approxCount = " + approxCount);
  System.out.println("realCount = " + realCount);
  assertFalse(result.getApproximateCount());
  assertEquals(approxCount, realCount);
}

代码示例来源：origin: opencb/opencga

@Test
public void testIncludeFiles() throws Exception {
  query = new Query()
      .append(VariantQueryParam.INCLUDE_STUDY.key(), "S_1")
      .append(VariantQueryParam.INCLUDE_FILE.key(), file12877);
  queryResult = query(query, options);
  assertEquals(dbAdaptor.count(null).first().intValue(), queryResult.getNumResults());
  for (Variant variant : queryResult.getResult()) {
    assertTrue(variant.getStudies().size() <= 1);
    StudyEntry s_1 = variant.getStudy("S_1");
    if (s_1 != null) {
      assertTrue(s_1.getFiles().size() <= 1);
      if (s_1.getFiles().size() == 1) {
        assertNotNull(s_1.getFile(file12877));
      }
    }
    assertTrue(variant.getStudies().size() <= 1);
  }
  assertThat(queryResult, everyResult(allOf(not(withStudy("S_2")), not(withStudy("S_3")), not(withStudy("S_4")))));
}

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

for (int i = 0; i < queryResult.getNumResults(); i++) {
  Variant variant1 = it_1.next();
  Variant variant2 = it_2.next();

代码示例来源：origin: opencb/opencga

.append(VariantQueryParam.STUDY.key(), "S_1");
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), allOf(
    .append(VariantQueryParam.STUDY.key(), "S_1");
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), anyOf(
    .append(VariantQueryParam.STUDY.key(), "S_1");
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), anyOf(
    .append(VariantQueryParam.STUDY.key(), "S_1");
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), is("LowGQX;LowMQ;LowQD;TruthSensitivityTranche99.90to100.00"))))));
    .append(VariantQueryParam.STUDY.key(), "S_1");
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(FILTER, fileEntry -> fileEntry.getAttributes().get(FILTER), anyOf(

代码示例来源：origin: opencb/opencga

.append(VariantQueryParam.FILE.key(), file12877);
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
System.out.println(allVariants.first().toJson());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    .append(VariantQueryParam.FILE.key(), file12877);
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(QUAL, fileEntry -> fileEntry.getAttributes().get(QUAL), allOf(notNullValue(), with("", Double::valueOf, lt(50))))))));
    .append(VariantQueryParam.FILE.key(), file12877);
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    with(QUAL, fileEntry -> fileEntry.getAttributes().get(QUAL), anyOf(with("", Double::valueOf, lt(5)), nullValue()))))));
    .append(VariantQueryParam.FILE.key(), file12877);
queryResult = query(query, options);
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", withFileId(file12877,
    allOf(

代码示例来源：origin: opencb/opencga

.append(FORMAT.key(), "NA12877:DP<100");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    withSamples("NA12877", "NA12878"),
    .append(FORMAT.key(), "NA12877:DP<100;GT=1/1");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    withSamples("NA12877", "NA12878"),
    .append(FORMAT.key(), "NA12877:DP<100;GT=1/1,0/1");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    withSamples("NA12877", "NA12878"),
    .append(FORMAT.key(), "NA12877:DP<100" + OR + "NA12878:DP<50");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    withSamples("NA12877", "NA12878"),
    .append(FORMAT.key(), "NA12877:DP<100" + AND + "NA12878:DP<50");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    withSamples("NA12877", "NA12878"),

代码示例来源：origin: opencb/opencga

+ ",1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    anyOf(
        + ",1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100");
queryResult = query(query, new QueryOptions());
System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
    anyOf(

代码示例来源：origin: opencb/opencga

@Test
public void testGetAllVariants_mixInfoFileOperators() {
  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(), file12877 + "," + file12878), options);
  thrown.expect(VariantQueryException.class);
  thrown.expectMessage(VariantQueryException.mixedAndOrOperators(FILE, INFO).getMessage());
  query = new Query(STUDY.key(), "S_1")
      .append(FILE.key(), file12877 + OR + file12878)
      .append(INFO.key(),
          "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz:HaplotypeScore<10"
              + AND
              + "1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100");
  queryResult = query(query, new QueryOptions());
  System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
  assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
      withFileId(file12877,
          withAttribute("HaplotypeScore", asNumber(lt(10)))
      ),
      withFileId(file12878,
          withAttribute("DP", asNumber(gt(100)))
      )
  ))));
}

代码示例来源：origin: opencb/opencga

@Test
public void testGetAllVariants_mixInfoFileOperators2() {
  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(), file12877 + "," + file12878), options);
  thrown.expect(VariantQueryException.class);
  thrown.expectMessage(VariantQueryException.mixedAndOrOperators(FILE, INFO).getMessage());
  query = new Query(STUDY.key(), "S_1")
      .append(FILE.key(), file12877 + AND + file12878)
      .append(INFO.key(),
          "1K.end.platinum-genomes-vcf-NA12877_S1.genome.vcf.gz:HaplotypeScore<10"
              + OR
              + "1K.end.platinum-genomes-vcf-NA12878_S1.genome.vcf.gz:DP>100");
  queryResult = query(query, new QueryOptions());
  System.out.println("queryResult.getNumResults() = " + queryResult.getNumResults());
  assertThat(queryResult, everyResult(allVariants, withStudy("S_1", allOf(
      withFileId(file12877),
      withFileId(file12878),
      anyOf(
          withFileId(file12877,
              withAttribute("HaplotypeScore", asNumber(lt(10)))
          ),
          withFileId(file12878,
              withAttribute("DP", asNumber(gt(100)))
          )
      )
  ))));
}

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VariantQueryResult类方法