org.opencb.commons.datastore.core.Query.getAsStringList()方法的使用及代码示例

x33g5p2x  于2022-01-28 转载在 其他  
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本文整理了Java中org.opencb.commons.datastore.core.Query.getAsStringList方法的一些代码示例，展示了Query.getAsStringList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.getAsStringList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：getAsStringList

Query.getAsStringList介绍

暂无

代码示例

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

public List<QueryResult> getPhenotypeGeneRelations(Query query, QueryOptions queryOptions) {
  Set<String> sourceContent = query.getAsStringList(QueryParams.SOURCE.key()) != null
      ? new HashSet<>(query.getAsStringList(QueryParams.SOURCE.key())) : null;
  List<QueryResult> queryResultList = new ArrayList<>();
  if (sourceContent == null || sourceContent.contains("clinvar")) {
    queryResultList.add(getClinvarPhenotypeGeneRelations(queryOptions));
  }
  if (sourceContent == null || sourceContent.contains("gwas")) {
    queryResultList.add(getGwasPhenotypeGeneRelations(queryOptions));
  }
  return queryResultList;
}

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

public List<QueryResult> getPhenotypeGeneRelations(Query query, QueryOptions queryOptions) {
  Set<String> sourceContent = query.getAsStringList(QueryParams.SOURCE.key()) != null
      ? new HashSet<>(query.getAsStringList(QueryParams.SOURCE.key())) : null;
  List<QueryResult> queryResultList = new ArrayList<>();
  if (sourceContent == null || sourceContent.contains("clinvar")) {
    queryResultList.add(getClinvarPhenotypeGeneRelations(queryOptions));
  }
  if (sourceContent == null || sourceContent.contains("gwas")) {
    queryResultList.add(getGwasPhenotypeGeneRelations(queryOptions));
  }
  return queryResultList;
}

代码示例来源：origin: opencb/cellbase

public List<QueryResult> getPhenotypeGeneRelations(Query query, QueryOptions queryOptions) {
  Set<String> sourceContent = query.getAsStringList(QueryParams.SOURCE.key()) != null
      ? new HashSet<>(query.getAsStringList(QueryParams.SOURCE.key())) : null;
  List<QueryResult> queryResultList = new ArrayList<>();
  if (sourceContent == null || sourceContent.contains("clinvar")) {
    queryResultList.add(getClinvarPhenotypeGeneRelations(queryOptions));
  }
  if (sourceContent == null || sourceContent.contains("gwas")) {
    queryResultList.add(getGwasPhenotypeGeneRelations(queryOptions));
  }
  return queryResultList;
}

代码示例来源：origin: opencb/cellbase

public List<QueryResult> getPhenotypeGeneRelations(Query query, QueryOptions queryOptions) {
  Set<String> sourceContent = query.getAsStringList(QueryParams.SOURCE.key()) != null
      ? new HashSet<>(query.getAsStringList(QueryParams.SOURCE.key())) : null;
  List<QueryResult> queryResultList = new ArrayList<>();
  if (sourceContent == null || sourceContent.contains("clinvar")) {
    queryResultList.add(getClinvarPhenotypeGeneRelations(queryOptions));
  }
  if (sourceContent == null || sourceContent.contains("gwas")) {
    queryResultList.add(getGwasPhenotypeGeneRelations(queryOptions));
  }
  return queryResultList;
}

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

private void createGeneOrQuery(Query query, String queryParam, List<Bson> andBsonList) {
  if (query != null) {
    List<String> geneList = query.getAsStringList(queryParam);
    if (geneList != null && !geneList.isEmpty()) {
      if (geneList.size() == 1) {
        andBsonList.add(getGeneQuery(geneList.get(0)));
      } else {
        List<Bson> orBsonList = new ArrayList<>(geneList.size());
        for (String geneId : geneList) {
          orBsonList.add(getGeneQuery(geneId));
        }
        andBsonList.add(Filters.or(orBsonList));
      }
    }
  }
}

代码示例来源：origin: opencb/cellbase

private void createGeneOrQuery(Query query, String queryParam, List<Bson> andBsonList) {
  if (query != null) {
    List<String> geneList = query.getAsStringList(queryParam);
    if (geneList != null && !geneList.isEmpty()) {
      if (geneList.size() == 1) {
        andBsonList.add(getGeneQuery(geneList.get(0)));
      } else {
        List<Bson> orBsonList = new ArrayList<>(geneList.size());
        for (String geneId : geneList) {
          orBsonList.add(getGeneQuery(geneId));
        }
        andBsonList.add(Filters.or(orBsonList));
      }
    }
  }
}

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;
}

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: org.opencb.cellbase/cellbase-lib

private void createClinvarTypeQuery(Query query, List<Bson> andBsonList) {
  if (query != null && query.getString(QueryParams.CLINVARTYPE.key()) != null
      && !query.getString(QueryParams.CLINVARTYPE.key()).isEmpty()) {
    createOrQuery(query.getAsStringList(QueryParams.CLINVARTYPE.key()).stream()
            .map((typeString) -> typeString.replace("_", " "))
            .collect(Collectors.toList()),
        "clinvarSet.referenceClinVarAssertion.measureSet.measure.type", andBsonList);
  }
}

代码示例来源：origin: opencb/cellbase

private void createClinvarTypeQuery(Query query, List<Bson> andBsonList) {
  if (query != null && query.getString(QueryParams.CLINVARTYPE.key()) != null
      && !query.getString(QueryParams.CLINVARTYPE.key()).isEmpty()) {
    createOrQuery(query.getAsStringList(QueryParams.CLINVARTYPE.key()).stream()
            .map((typeString) -> typeString.replace("_", " "))
            .collect(Collectors.toList()),
        "clinvarSet.referenceClinVarAssertion.measureSet.measure.type", andBsonList);
  }
}

代码示例来源：origin: opencb/cellbase

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: org.opencb.cellbase/cellbase-lib

private void createClinvarReviewQuery(Query query, List<Bson> andBsonList) {
  if (query != null && query.getString(QueryParams.CLINVARREVIEW.key()) != null
      && !query.getString(QueryParams.CLINVARREVIEW.key()).isEmpty()) {
    createOrQuery(query.getAsStringList(QueryParams.CLINVARREVIEW.key()).stream()
            .map(String::toUpperCase)
            .collect(Collectors.toList()),
        "clinvarSet.referenceClinVarAssertion.clinicalSignificance.reviewStatus", andBsonList);
  }
}

代码示例来源：origin: opencb/cellbase

private void createClinvarReviewQuery(Query query, List<Bson> andBsonList) {
  if (query != null && query.getString(QueryParams.CLINVARREVIEW.key()) != null
      && !query.getString(QueryParams.CLINVARREVIEW.key()).isEmpty()) {
    createOrQuery(query.getAsStringList(QueryParams.CLINVARREVIEW.key()).stream()
            .map(String::toUpperCase)
            .collect(Collectors.toList()),
        "clinvarSet.referenceClinVarAssertion.clinicalSignificance.reviewStatus", andBsonList);
  }
}

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/cellbase

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

private void fixQueryObject(Study study, Query query, String sessionId) throws CatalogException {
  if (query.containsKey("inputFiles")) {
    MyResources<File> resource = catalogManager.getFileManager().getUids(query.getAsStringList("inputFiles"), study.getFqn(),
        sessionId);
    query.put(JobDBAdaptor.QueryParams.INPUT_UID.key(), resource.getResourceList().stream().map(File::getUid)
        .collect(Collectors.toList()));
    query.remove("inputFiles");
  }
  if (query.containsKey("outputFiles")) {
    MyResources<File> resource = catalogManager.getFileManager().getUids(query.getAsStringList("outputFiles"), study.getFqn(),
        sessionId);
    query.put(JobDBAdaptor.QueryParams.OUTPUT_UID.key(), resource.getResourceList().stream().map(File::getUid)
        .collect(Collectors.toList()));
    query.remove("outputFiles");
  }
}

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

void fixQueryObject(Study study, Query query, String sessionId) throws CatalogException {
  if (StringUtils.isNotEmpty(query.getString(FileDBAdaptor.QueryParams.ID.key()))) {
    MyResources<File> uids = getUids(query.getAsStringList(FileDBAdaptor.QueryParams.ID.key()), study.getFqn(), sessionId);
    query.remove(FileDBAdaptor.QueryParams.ID.key());
    query.put(FileDBAdaptor.QueryParams.UID.key(), uids.getResourceList().stream().map(File::getUid).collect(Collectors.toList()));
  }
  // The samples introduced could be either ids or names. As so, we should use the smart resolutor to do this.
  if (StringUtils.isNotEmpty(query.getString(FileDBAdaptor.QueryParams.SAMPLES.key()))) {
    MyResources<Sample> resource = catalogManager.getSampleManager().getUids(
        query.getAsStringList(FileDBAdaptor.QueryParams.SAMPLES.key()), study.getFqn(), sessionId);
    query.put(FileDBAdaptor.QueryParams.SAMPLE_UIDS.key(), resource.getResourceList().stream().map(Sample::getUid)
        .collect(Collectors.toList()));
    query.remove(FileDBAdaptor.QueryParams.SAMPLES.key());
  }
}

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 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));
}

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