本文整理了Java中org.opencb.commons.datastore.core.Query.toJson方法的一些代码示例，展示了Query.toJson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。Query.toJson方法的具体详情如下：
包路径：org.opencb.commons.datastore.core.Query
类名称：Query
方法名：toJson

Query.toJson介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

private void display(Query query, QueryOptions queryOptions, SolrQuery solrQuery) {
    System.out.println("Query        : " + query.toJson());
    System.out.println("Query options: " + queryOptions.toJson());
    System.out.println("Solr query   : " + solrQuery.toString());
    System.out.println();
  }
}

代码示例来源：origin: opencb/opencga

private void checkCanExecuteNativeQuery(Query query) {
  String message = "Query " + (query == null ? null : query.toJson()) + " is not fully supported";
  try {
    assumeTrue(message, VariantHBaseQueryParser.isSupportedQuery(query));
  } catch (AssumptionViolatedException e) {
    System.out.println(message);
    throw e;
  }
}

代码示例来源：origin: opencb/opencga

@Override
public VariantQueryResult<Variant> get(Query query, QueryOptions options) {
  logger.info("Query " + query.toJson());
  logger.info("QueryOptions " + options.toJson());
  logger.info("dbName " + dbName);
  List<Variant> variants = new ArrayList<>();
  iterator(query, options).forEachRemaining(variants::add);
  return new VariantQueryResult<>("", 0, variants.size(), variants.size(), "", "", variants, null,
      DummyVariantStorageEngine.STORAGE_ENGINE_ID);
}

代码示例来源：origin: opencb/opencga

logger.info("Query : {} ", query.toJson());
annotationFile = createAnnotation(
    Paths.get(params.getString(OUT_DIR, "/tmp")),

代码示例来源：origin: opencb/opencga

throw e;
} else {
  throw new CatalogDBException("Error parsing query : " + query.toJson(), e);

代码示例来源：origin: opencb/opencga

protected void check(String collection, Query query, QueryOptions options) throws StorageEngineException {
  assertEquals(query.toJson() + " " + options.toJson(), collection, VariantSearchUtils.inferSpecificSearchIndexSamplesCollection(query, options, variantStorageEngine.getStudyConfigurationManager(), DB_NAME));
}

代码示例来源：origin: opencb/opencga

@Test
public void queriesWithRelease() throws Exception {
  System.out.println(queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(VariantQueryParam.SAMPLE.key(), "sample2").append(VariantQueryParam.RELEASE.key(), 2), sessionId).toJson());
  System.out.println(queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(VariantQueryParam.SAMPLE.key(), "sample2").append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson());
  System.out.println(queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(VariantQueryParam.INCLUDE_SAMPLE.key(), "sample2").append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson());
  System.out.println(queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(VariantQueryParam.FILE.key(), "file1.vcf").append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson());
  System.out.println(queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(VariantQueryParam.STATS_MAF.key(), "c1>0.1").append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson());
  System.out.println(queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(VariantQueryParam.GENOTYPE.key(), "sample1:HOM_ALT,sample2:HET_REF").append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson());
}

代码示例来源：origin: opencb/opencga

private void queryGeneCT(String gene, String so, Query query, Matcher<VariantAnnotation> regionMatcher) {
    logger.info(query.toJson());
    queryResult = query(query, null);
    logger.info(" -> numResults " + queryResult.getNumResults());

    Matcher<String> geneMatcher;
    List<String> genes = Arrays.asList(gene.split(","));
    if (gene.contains(",")) {
      geneMatcher = anyOf(genes.stream().map(CoreMatchers::is).collect(Collectors.toList()));
    } else {
      geneMatcher = is(gene);
    }
    assertThat(queryResult, everyResult(allVariants, hasAnnotation(
        anyOf(
            allOf(
                hasAnyGeneOf(genes),
                withAny("consequence type", VariantAnnotation::getConsequenceTypes, allOf(
                    with("gene", ConsequenceType::getGeneName, geneMatcher),
                    withAny("SO", ConsequenceType::getSequenceOntologyTerms,
                        with("accession", SequenceOntologyTerm::getAccession, is(so))))))
            ,
            allOf(
                regionMatcher,
//                                not(hasAnyGeneOf(genes)),
                hasSO(hasItem(so))
        )))));
  }

代码示例来源：origin: opencb/opencga

result.setResponseMessage(query.toJson());
result.setResponseCodeOK();
result.sampleStart();

代码示例来源：origin: opencb/opencga

protected VariantQueryResult<Variant> query(Query query, QueryOptions options) {
  try {
    query = preProcessQuery(query, options);
    StudyConfigurationManager scm = dbAdaptor.getStudyConfigurationManager();
    String collection = VariantSearchUtils.inferSpecificSearchIndexSamplesCollection(query, options, scm, DB_NAME);
    // Do not execute this test if the query is not covered by the specific search index collection
    Assume.assumeThat(query.toJson(), collection, CoreMatchers.notNullValue());
    if (options.getInt(QueryOptions.LIMIT, 0) <= 0) {
      options = new QueryOptions(options);
      options.put(QueryOptions.LIMIT, 100000);
    }
    return variantStorageEngine.getVariantSearchManager().query(collection, query, options);
  } catch (StorageEngineException | VariantSearchException | IOException e) {
    e.printStackTrace();
    Assert.fail(e.getMessage());
  }
  return null;
}

代码示例来源：origin: opencb/opencga

@Test
public void fileWrongNameWithRelease() throws Exception {
  thrown.expectMessage("not found");
  thrown.expect(CatalogException.class);
  queryUtils.parseQuery(new Query(VariantQueryParam.FILE.key(), "non_existing_file.vcf")
      .append(VariantQueryParam.STUDY.key(), "s1"), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void includeSampleWrongRelease() throws Exception {
  VariantQueryException e = VariantCatalogQueryUtils.wrongReleaseException(VariantQueryParam.INCLUDE_SAMPLE, "sample3", 1);
  thrown.expectMessage(e.getMessage());
  thrown.expect(e.getClass());
  queryUtils.parseQuery(new Query(VariantQueryParam.INCLUDE_SAMPLE.key(), "sample3")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void fileWrongRelease() throws Exception {
  VariantQueryException e = VariantCatalogQueryUtils.wrongReleaseException(VariantQueryParam.FILE, "file3.vcf", 1);
  thrown.expectMessage(e.getMessage());
  thrown.expect(e.getClass());
  queryUtils.parseQuery(new Query(VariantQueryParam.FILE.key(), "file3.vcf")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void cohortWrongRelease() throws Exception {
  VariantQueryException e = VariantCatalogQueryUtils.wrongReleaseException(VariantQueryParam.COHORT, "c2", 1);
  thrown.expectMessage(e.getMessage());
  thrown.expect(e.getClass());
  queryUtils.parseQuery(new Query(VariantQueryParam.COHORT.key(), "c2")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void sampleWrongRelease() throws Exception {
  VariantQueryException e = VariantCatalogQueryUtils.wrongReleaseException(VariantQueryParam.SAMPLE, "sample3", 1);
  thrown.expectMessage(e.getMessage());
  thrown.expect(e.getClass());
  queryUtils.parseQuery(new Query(VariantQueryParam.SAMPLE.key(), "sample3")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void cohortStatsWrongRelease() throws Exception {
  VariantQueryException e = VariantCatalogQueryUtils.wrongReleaseException(VariantQueryParam.STATS_MAF, "c2", 1);
  thrown.expectMessage(e.getMessage());
  thrown.expect(e.getClass());
  queryUtils.parseQuery(new Query(VariantQueryParam.STATS_MAF.key(), "c2>0.2")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void includeFileWrongRelease() throws Exception {
  VariantQueryException e = VariantCatalogQueryUtils.wrongReleaseException(VariantQueryParam.INCLUDE_FILE, "file3.vcf", 1);
  thrown.expectMessage(e.getMessage());
  thrown.expect(e.getClass());
  queryUtils.parseQuery(new Query(VariantQueryParam.INCLUDE_FILE.key(), "file3.vcf")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void sampleNotFound() throws Exception {
  thrown.expectMessage("not found");
  thrown.expect(CatalogException.class);
  queryUtils.parseQuery(new Query(VariantQueryParam.SAMPLE.key(), "sample_not_exists")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void fileNotFound() throws Exception {
  thrown.expectMessage("not found");
  thrown.expect(CatalogException.class);
  queryUtils.parseQuery(new Query(VariantQueryParam.FILE.key(), "non_existing_file.vcf")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}

代码示例来源：origin: opencb/opencga

@Test
public void fileNotIndexed() throws Exception {
  thrown.expectMessage("not indexed");
  thrown.expect(VariantQueryException.class);
  queryUtils.parseQuery(new Query(VariantQueryParam.FILE.key(), "file5.vcf")
      .append(VariantQueryParam.STUDY.key(), "s1")
      .append(VariantQueryParam.RELEASE.key(), 1), sessionId).toJson();
}