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

Query介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

public VariantQueryResult<Variant> intersect(Query query, QueryOptions queryOptions, List<String> studyIds, String sessionId)
    throws CatalogException, IOException, StorageEngineException {
  Query intersectQuery = new Query(query);
  intersectQuery.put(VariantQueryParam.STUDY.key(), String.join(VariantQueryUtils.AND, studyIds));
  return get(intersectQuery, queryOptions, sessionId);
}

代码示例来源：origin: opencb/opencga

@Override
public QueryResult<Individual> get(long individualId, QueryOptions options, String userId)
    throws CatalogDBException, CatalogAuthorizationException {
  long studyId = getStudyId(individualId);
  Query query = new Query()
      .append(QueryParams.UID.key(), individualId)
      .append(QueryParams.STUDY_UID.key(), studyId)
      .append(QueryParams.STATUS_NAME.key(), "!=" + Status.DELETED);
  return get(query, options, userId);
}

代码示例来源：origin: org.opencb.cellbase/cellbase-lib

private void createClinvarClinicalSignificanceQuery(Query query, List<Bson> andBsonList) {
  if (query != null && query.getString(QueryParams.CLINVARCLINSIG.key()) != null
      && !query.getString(QueryParams.CLINVARCLINSIG.key()).isEmpty()) {
    createOrQuery(query.getAsStringList(QueryParams.CLINVARCLINSIG.key()).stream()
            .map((clinicalSignificanceString) -> clinicalSignificanceString.replace("_", " "))
            .collect(Collectors.toList()),
        "clinvarSet.referenceClinVarAssertion.clinicalSignificance.description", andBsonList);
  }
}

代码示例来源：origin: opencb/opencga

/**
 * Checks if the query contains any annotation query.
 *
 * @param query Query object.
 * @return whether query contains an annotation query or not.
 */
public boolean containsAnnotationQuery(Query query) {
  if (query == null || query.isEmpty()) {
    return false;
  }
  return query.containsKey(Constants.ANNOTATION);
}

代码示例来源：origin: org.opencb.cellbase/cellbase-lib

private void createImprecisePositionQuery(Query query, String leftQueryParam, String rightQueryParam,
                     String leftLimitMongoField, String righLimitMongoField,
                     List<Bson> andBsonList) {
  if (query != null && query.getString(leftQueryParam) != null && !query.getString(leftQueryParam).isEmpty()
      && query.getString(rightQueryParam) != null && !query.getString(rightQueryParam).isEmpty()) {
    int leftQueryValue = query.getInt(leftQueryParam);
    int rightQueryValue = query.getInt(rightQueryParam);
    andBsonList.add(Filters.lte(leftLimitMongoField, rightQueryValue));
    andBsonList.add(Filters.gte(righLimitMongoField, leftQueryValue));
  }
}

代码示例来源：origin: org.opencb.cellbase/cellbase-lib

protected void createOrQuery(Query query, String queryParam, String mongoDbField, List<Bson> andBsonList,
               QueryValueType queryValueType) {
  if (query != null && query.getString(queryParam) != null && !query.getString(queryParam).isEmpty()) {
    switch (queryValueType) {
      case INTEGER:
        createOrQuery(query.getAsIntegerList(queryParam), mongoDbField, andBsonList);
        break;
      default:
        createOrQuery(query.getAsStringList(queryParam), mongoDbField, andBsonList);
    }
  }
}

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 filterOutDeleted(Query query) {
  if (!query.containsKey(QueryParams.STATUS_NAME.key())) {
    query.append(QueryParams.STATUS_NAME.key(), "!=" + Status.DELETED);
  }
}

代码示例来源：origin: opencb/opencga

@Test
public void queryByFamily() throws Exception {
  Query query = queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(FAMILY.key(), "f1"), sessionId);
  assertEquals(Arrays.asList("sample1", "sample2", "sample3", "sample4"), query.getAsStringList(SAMPLE.key()));
  assertFalse(VariantQueryUtils.isValidParam(query, GENOTYPE));
  query = queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(FAMILY.key(), "f1").append(MODE_OF_INHERITANCE.key(), "MONOALLELIC"), sessionId);
  assertEquals("sample3:0/1,1/1;sample4:0/0;sample1:0/0;sample2:0/0", query.getString(GENOTYPE.key()));
  assertFalse(VariantQueryUtils.isValidParam(query, SAMPLE));
}

代码示例来源：origin: opencb/opencga

@Override
public void delete(long id) throws CatalogDBException {
  Query query = new Query(QueryParams.ID.key(), id);
  delete(query);
}

代码示例来源：origin: opencb/opencga

private void fixQueryObject(Study study, Query query, String sessionId) throws CatalogException {
  // The individuals introduced could be either ids or names. As so, we should use the smart resolutor to do this.
  if (StringUtils.isNotEmpty(query.getString(SampleDBAdaptor.QueryParams.INDIVIDUAL.key()))) {
    MyResources<Individual> resource = catalogManager.getIndividualManager().getUids(
        query.getAsStringList(SampleDBAdaptor.QueryParams.INDIVIDUAL.key()), study.getFqn(), sessionId);
    query.put(SampleDBAdaptor.QueryParams.INDIVIDUAL_UID.key(), resource.getResourceList().stream().map(Individual::getUid)
        .collect(Collectors.toList()));
    query.remove(SampleDBAdaptor.QueryParams.INDIVIDUAL.key());
  }
}

代码示例来源：origin: opencb/opencga

private Document getStudyDocument(Query query) throws CatalogDBException {
    // Get the study document
    Query studyQuery = new Query()
        .append(StudyDBAdaptor.QueryParams.UID.key(), query.getLong(FamilyDBAdaptor.QueryParams.STUDY_UID.key()));
    QueryResult<Document> queryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(studyQuery, QueryOptions.empty());
    if (queryResult.getNumResults() == 0) {
      throw new CatalogDBException("Study " + query.getLong(FamilyDBAdaptor.QueryParams.STUDY_UID.key()) + " not found");
    }
    return queryResult.first();
  }
}

代码示例来源：origin: opencb/opencga

private void fixQueryObject(Study study, Query query, String sessionId) throws CatalogException {
  if (query.containsKey(CohortDBAdaptor.QueryParams.SAMPLES.key())) {
    // First look for the sample ids.
    MyResources<Sample> samples = catalogManager.getSampleManager()
        .getUids(query.getAsStringList(CohortDBAdaptor.QueryParams.SAMPLES.key()), study.getFqn(), sessionId);
    query.remove(CohortDBAdaptor.QueryParams.SAMPLES.key());
    query.append(CohortDBAdaptor.QueryParams.SAMPLE_UIDS.key(), samples.getResourceList().stream().map(Sample::getUid)
        .collect(Collectors.toList()));
  }
}

代码示例来源：origin: opencb/opencga

@Test
public void queryByPanel() throws Exception {
  Query query = queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(PANEL.key(), "MyPanel"), sessionId);
  assertEquals(Arrays.asList("BRCA2","CADM1","CTBP2P1","ADSL"), query.getAsList(GENE.key()));
  query = queryUtils.parseQuery(new Query(STUDY.key(), "s1").append(PANEL.key(), "MyPanel").append(GENE.key(), "ASDF"), sessionId);
  assertEquals(Arrays.asList("BRCA2","CADM1","CTBP2P1","ADSL", "ASDF"), query.getAsList(GENE.key()));
}

代码示例来源：origin: opencb/cellbase

private void createPhenotypeQuery(Query query, List<Bson> andBsonList) {
  if (query != null && query.getString(QueryParams.TRAIT.key()) != null
      && !query.getString(QueryParams.TRAIT.key()).isEmpty()) {
    andBsonList.add(Filters.text(query.getString(QueryParams.TRAIT.key())));
  }
}

代码示例来源：origin: opencb/opencga

public Project getProjectFromQuery(Query query, String sessionId, QueryOptions options) throws CatalogException {
  if (isValidParam(query, VariantCatalogQueryUtils.PROJECT)) {
    String project = query.getString(VariantCatalogQueryUtils.PROJECT.key());
    return catalogManager.getProjectManager().get(project, options, sessionId).first();
  } else {
    String studyFqn = getAnyStudy(query, sessionId);
    String project = catalogManager.getStudyManager().getProjectFqn(studyFqn);
    return catalogManager.getProjectManager().get(new Query(ProjectDBAdaptor.QueryParams.FQN.key(), project), options, sessionId)
        .first();
  }
}

代码示例来源：origin: opencb/opencga

private Document getStudyDocument(Query query) throws CatalogDBException {
  // Get the study document
  Query studyQuery = new Query(StudyDBAdaptor.QueryParams.UID.key(), query.getLong(QueryParams.STUDY_UID.key()));
  QueryResult<Document> queryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(studyQuery, QueryOptions.empty());
  if (queryResult.getNumResults() == 0) {
    throw new CatalogDBException("Study " + query.getLong(QueryParams.STUDY_UID.key()) + " not found");
  }
  return queryResult.first();
}

代码示例来源：origin: opencb/opencga

@Test
public void parseSampleAnnotationQuery() throws Exception {
  Query query = CatalogUtils.parseSampleAnnotationQuery("age>20;" + SampleDBAdaptor.QueryParams.PHENOTYPES.key() + "=hpo:123,hpo:456;" + SampleDBAdaptor.QueryParams.ID.key() + "=smith", SampleDBAdaptor.QueryParams::getParam);
  assertEquals(3, query.size());
  assertTrue(query.containsKey(SampleDBAdaptor.QueryParams.ID.key()));
  assertEquals("=smith", query.getString(SampleDBAdaptor.QueryParams.ID.key()));
  assertTrue(query.containsKey(SampleDBAdaptor.QueryParams.ANNOTATION.key()));
  assertEquals("annotation.age>20", query.getString(SampleDBAdaptor.QueryParams.ANNOTATION.key()));
  assertTrue(query.containsKey(SampleDBAdaptor.QueryParams.PHENOTYPES.key()));
  assertEquals("=hpo:123,hpo:456", query.getString(SampleDBAdaptor.QueryParams.PHENOTYPES.key()));
}

代码示例来源：origin: opencb/opencga

private List<String> getStudyIds(String userId, Query query) throws CatalogException {
  List<String> studyIds = new ArrayList<>();
  if (query != null && query.containsKey(ClinicalVariantEngine.QueryParams.STUDY.key())) {
    String study = query.getString(ClinicalVariantEngine.QueryParams.STUDY.key());
    List<String> studies = Arrays.asList(study.split(","));
    studyIds = catalogManager.getStudyManager().resolveIds(studies, userId)
        .stream()
        .map(Study::getFqn)
        .collect(Collectors.toList());
  }
  return studyIds;
}

代码示例来源：origin: org.opencb.commons/commons-datastore-mongodb

public static Bson createAutoFilter(String mongoDbField, String queryParam, Query query, QueryParam.Type type)
    throws NumberFormatException {
  Bson filter = null;
  if (query != null && query.containsKey(queryParam)) {
    List<String> values = query.getAsStringList(queryParam);
    LogicalOperator operator = LogicalOperator.OR;
    if (values.size() == 1) {
      operator = checkOperator(values.get(0));
    }
    filter = createAutoFilter(mongoDbField, queryParam, query, type, operator);
  }
  return filter;
}