本文整理了Java中org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.isValidParam()方法的一些代码示例，展示了VariantQueryUtils.isValidParam()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。VariantQueryUtils.isValidParam()方法的具体详情如下：
包路径：org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils
类名称：VariantQueryUtils
方法名：isValidParam

VariantQueryUtils.isValidParam介绍

[英]Check if the object query contains the value param, is not null and, if is an string or a list, is not empty.

isValidParam(new Query(), PARAM) == false isValidParam(new Query(PARAM.key(), null), PARAM) == false isValidParam(new Query(PARAM.key(), ""), PARAM) == false isValidParam(new Query(PARAM.key(), Collections.emptyList()), PARAM) == false isValidParam(new Query(PARAM.key(), 5), PARAM) == true isValidParam(new Query(PARAM.key(), "sdfas"), PARAM) == true
[中]检查对象查询是否包含值param，是否不为null，如果是字符串或列表，是否不为空。
isValidParam（new Query（），PARAM）==false isValidParam（new Query（PARAM.key（），null），PARAM）==false isValidParam（new Query（PARAM.key（），“”），PARAM）==false isValidParam（new Query（PARAM.key（），Collections）。emptyList（）、PARAM）=false-isValidParam（新查询（PARAM.key（）、5）、PARAM）==true-isValidParam（新查询（PARAM.key（）、“sdfas”）、PARAM）==true

代码示例

代码示例来源：origin: opencb/opencga

public static boolean isQueryCovered(Query query) {
  for (VariantQueryParam nonCoveredParam : UNSUPPORTED_QUERY_PARAMS) {
    if (isValidParam(query, nonCoveredParam)) {
      return false;
    }
  }
  return true;
}

代码示例来源：origin: opencb/opencga

private void unsupportedFilter(Query query, VariantQueryParam param) {
    if (isValidParam(query, param)) {
      String warn = "Unsupported filter \"" + param + "\"";
//            warnings.add(warn);
      logger.warn(warn);
    }
  }

代码示例来源：origin: opencb/opencga

public static boolean isIncludeFilesDefined(Query query, Set<VariantField> fields) {
  if (getIncludeFilesList(query, fields) != null) {
    return true;
  }
  return isValidParam(query, SAMPLE, true) || isValidParam(query, INCLUDE_SAMPLE, false) || isValidParam(query, GENOTYPE, false);
}

代码示例来源：origin: opencb/opencga

public static boolean isIncludeSamplesDefined(Query query, Set<VariantField> fields) {
  if (getIncludeSamplesList(query, fields) != null) {
    return true;
  }
  return isValidParam(query, FILE, true) || isValidParam(query, INCLUDE_FILE, true);
}

代码示例来源：origin: opencb/opencga

@Override
protected QueryOptions getIteratorQueryOptions(Query query, ObjectMap params) {
  QueryOptions iteratorQueryOptions = super.getIteratorQueryOptions(query, params);
  if (!VariantQueryUtils.isValidParam(query, VariantQueryParam.FILE)
      || !VariantQueryUtils.isValidParam(query, VariantQueryParam.ANNOTATION_EXISTS)) {
    iteratorQueryOptions.putIfAbsent(VariantHadoopDBAdaptor.NATIVE, true);
  }
  return iteratorQueryOptions;
}

代码示例来源：origin: opencb/opencga

public static Set<VariantQueryParam> validParams(Query query) {
  Set<VariantQueryParam> params = new HashSet<>(query == null ? 0 : query.size());
  for (VariantQueryParam queryParam : values()) {
    if (isValidParam(query, queryParam)) {
      params.add(queryParam);
    }
  }
  return params;
}

代码示例来源：origin: opencb/opencga

private boolean doHBaseColumnIntersect(Query query, QueryOptions options) {
  return options.getBoolean("hbase_column_intersect", true)
      // && !options.getBoolean(VariantHadoopDBAdaptor.NATIVE)
      && (isValidParam(query, SAMPLE) && isSupportedQueryParam(query, SAMPLE)
      || isValidParam(query, FILE) && isSupportedQueryParam(query, FILE)
      || isValidParam(query, GENOTYPE) && isSupportedQueryParam(query, GENOTYPE)
      && parseGenotypeFilter(query.getString(GENOTYPE.key()), new HashMap<>()) != QueryOperation.OR);
}

代码示例来源：origin: opencb/opencga

private List<Region> getRegions(Query query) {
  List<Region> regions = new ArrayList<>();
  if (isValidParam(query, REGION)) {
    regions.addAll(Region.parseRegions(query.getString(REGION.key())));
  }
  if (isValidParam(query, ANNOT_GENE_REGIONS)) {
    regions.addAll(Region.parseRegions(query.getString(ANNOT_GENE_REGIONS.key())));
  }
  regions = mergeRegions(regions);
  return regions;
}

代码示例来源：origin: opencb/opencga

private String buildOutputFileName(String alias, Query query) {
    List<Region> regions = new ArrayList<>();
    if (VariantQueryUtils.isValidParam(query, VariantQueryParam.REGION)) {
      List<Region> c = Region.parseRegions(query.getString(VariantQueryParam.REGION.key()));
      if (c != null) {
        regions.addAll(c);
      }
    }
    if (regions.isEmpty() || regions.size() > 1) {
      return alias + '.' + TimeUtils.getTime();
    } else {
      return alias + ".region_" + regions.get(0).toString() + '.' + TimeUtils.getTime();
    }
  }
}

代码示例来源：origin: opencb/opencga

public static boolean isValidParam(Query query, QueryParam param, boolean discardNegated) {
  boolean validParam = isValidParam(query, param);
  if (!discardNegated || !validParam) {
    return validParam;
  } else {
    String strValue = query.getString(param.key());
    return splitValue(strValue, checkOperator(strValue))
        .stream()
        .anyMatch((v) -> !isNegated(v)); // Discard negated
  }
}

代码示例来源：origin: opencb/opencga

public static boolean isOutputMultiStudy(Query query, QueryOptions options, Collection<?> studies) {
  Set<VariantField> fields = VariantField.getIncludeFields(options);
  if (!fields.contains(VariantField.STUDIES)) {
    return false;
  } else if (isValidParam(query, INCLUDE_STUDY)) {
    String includeStudy = query.getString(VariantQueryParam.INCLUDE_STUDY.key());
    if (NONE.equals(includeStudy)) {
      return false;
    } else if (ALL.equals(includeStudy)) {
      return studies.size() > 1;
    } else {
      return query.getAsList(VariantQueryParam.INCLUDE_STUDY.key()).size() > 1;
    }
  } else if (isValidParam(query, STUDY)) {
    String value = query.getString(VariantQueryParam.STUDY.key());
    long numStudies = splitValue(value, checkOperator(value)).stream().filter(s -> !isNegated(s)).count();
    return numStudies > 1;
  } else {
    return studies.size() > 1;
  }
}

代码示例来源：origin: opencb/opencga

@Override
protected boolean doIntersectWithSearch(Query query, QueryOptions options) throws StorageEngineException {
  boolean doIntersectWithSearch = super.doIntersectWithSearch(query, options);
  if (doIntersectWithSearch) {
    if (!isValidParam(query, VariantQueryParam.ANNOT_TRAIT)
        && VariantStorageEngine.UseSearchIndex.from(options).equals(VariantStorageEngine.UseSearchIndex.AUTO)
        && doHBaseSampleIndexIntersect(query, options)) {
      return false;
    }
  }
  return doIntersectWithSearch;
}

代码示例来源：origin: opencb/opencga

public static void convertExpressionToGeneQuery(Query query, CellBaseUtils cellBaseUtils) {
    if (isValidParam(query, VariantQueryParam.ANNOT_EXPRESSION)) {
      String value = query.getString(VariantQueryParam.ANNOT_EXPRESSION.key());
      // Check if comma separated of semi colon separated (AND or OR)
      VariantQueryUtils.QueryOperation queryOperation = checkOperator(value);
      // Split by comma or semi colon
      List<String> expressionValues = splitValue(value, queryOperation);

      if (queryOperation == VariantQueryUtils.QueryOperation.AND) {
        throw VariantQueryException.malformedParam(VariantQueryParam.ANNOT_EXPRESSION, value, "Unimplemented AND operator");
      }
//            query.remove(VariantQueryParam.ANNOT_EXPRESSION.key());
      Set<String> genesByExpression = cellBaseUtils.getGenesByExpression(expressionValues);
      if (genesByExpression.isEmpty()) {
        genesByExpression = Collections.singleton(NONE);
      }
      query.put(ANNOT_EXPRESSION_GENES.key(), genesByExpression);
    }
  }

代码示例来源：origin: opencb/opencga

public static void convertGoToGeneQuery(Query query, CellBaseUtils cellBaseUtils) {
    if (isValidParam(query, VariantQueryParam.ANNOT_GO)) {
      String value = query.getString(VariantQueryParam.ANNOT_GO.key());
      // Check if comma separated of semi colon separated (AND or OR)
      VariantQueryUtils.QueryOperation queryOperation = checkOperator(value);
      // Split by comma or semi colon
      List<String> goValues = splitValue(value, queryOperation);

      if (queryOperation == VariantQueryUtils.QueryOperation.AND) {
        throw VariantQueryException.malformedParam(VariantQueryParam.ANNOT_GO, value, "Unimplemented AND operator");
      }
//            query.remove(VariantQueryParam.ANNOT_GO.key());
      Set<String> genesByGo = cellBaseUtils.getGenesByGo(goValues);
      if (genesByGo.isEmpty()) {
        genesByGo = Collections.singleton(NONE);
      }
      query.put(ANNOT_GO_GENES.key(), genesByGo);
    }
  }

代码示例来源：origin: opencb/opencga

@Test
public void testIsValid() {
  assertFalse(isValidParam(new Query(), ANNOTATION_EXISTS));
  assertFalse(isValidParam(new Query(ANNOTATION_EXISTS.key(), null), ANNOTATION_EXISTS));
  assertFalse(isValidParam(new Query(ANNOTATION_EXISTS.key(), ""), ANNOTATION_EXISTS));
  assertFalse(isValidParam(new Query(ANNOTATION_EXISTS.key(), Collections.emptyList()), ANNOTATION_EXISTS));
  assertFalse(isValidParam(new Query(ANNOTATION_EXISTS.key(), Arrays.asList()), ANNOTATION_EXISTS));
  assertTrue(isValidParam(new Query(ANNOTATION_EXISTS.key(), Arrays.asList(1,2,3)), ANNOTATION_EXISTS));
  assertTrue(isValidParam(new Query(ANNOTATION_EXISTS.key(), 5), ANNOTATION_EXISTS));
  assertTrue(isValidParam(new Query(ANNOTATION_EXISTS.key(), "sdfas"), ANNOTATION_EXISTS));
}

代码示例来源：origin: opencb/opencga

public static Query getEngineQuery(Query query, QueryOptions options, StudyConfigurationManager scm) throws StorageEngineException {
  Collection<VariantQueryParam> uncoveredParams = uncoveredParams(query);
  Query engineQuery = new Query();
  for (VariantQueryParam uncoveredParam : uncoveredParams) {
    engineQuery.put(uncoveredParam.key(), query.get(uncoveredParam.key()));
  }
  // Despite STUDIES is a covered filter, it has to be in the underlying
  // query to be used as defaultStudy
  if (isValidParam(query, STUDY)) {
    if (!uncoveredParams.isEmpty()) {
      // This will set the default study, if needed
      engineQuery.put(STUDY.key(), query.get(STUDY.key()));
    } else if (!isValidParam(query, INCLUDE_STUDY)) {
      // If returned studies is not defined, we need to define it with the values from STUDIES
      List<Integer> studies = VariantQueryUtils.getIncludeStudies(query, options, scm);
      engineQuery.put(INCLUDE_STUDY.key(), studies);
    }
  }
  return engineQuery;
}

代码示例来源：origin: opencb/opencga

@Override
public Query preProcessQuery(Query originalQuery, QueryOptions options) throws StorageEngineException {
  Query query = super.preProcessQuery(originalQuery, options);
  StudyConfigurationManager studyConfigurationManager = getStudyConfigurationManager();
  List<String> studyNames = studyConfigurationManager.getStudyNames(QueryOptions.empty());
  CellBaseUtils cellBaseUtils = getCellBaseUtils();
  if (isValidParam(query, STUDY) && studyNames.size() == 1) {
    query.remove(STUDY.key());
  }
  convertGoToGeneQuery(query, cellBaseUtils);
  convertExpressionToGeneQuery(query, cellBaseUtils);
  convertGenesToRegionsQuery(query, cellBaseUtils);
  return query;
}

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

public Integer getReleaseFilter(Query query, String sessionId) throws CatalogException {
  Integer release;
  if (isValidParam(query, VariantQueryParam.RELEASE)) {
    release = query.getInt(VariantQueryParam.RELEASE.key(), -1);
    if (release <= 0) {
      throw VariantQueryException.malformedParam(VariantQueryParam.RELEASE, query.getString(VariantQueryParam.RELEASE.key()));
    }
    Project project = getProjectFromQuery(query, sessionId,
        new QueryOptions(INCLUDE, ProjectDBAdaptor.QueryParams.CURRENT_RELEASE.key()));
    int currentRelease = project.getCurrentRelease();
    if (release > currentRelease) {
      throw VariantQueryException.malformedParam(VariantQueryParam.RELEASE, query.getString(VariantQueryParam.RELEASE.key()));
    } else if (release == currentRelease) {
      // Using latest release. We don't need to filter by release!
      release = null;
    } // else, filter by release
  } else {
    release = null;
  }
  return release;
}

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));
}