本文整理了Java中org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.checkOperator()方法的一些代码示例，展示了VariantQueryUtils.checkOperator()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.checkOperator()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：checkOperator

VariantQueryUtils.checkOperator介绍

[英]Checks that the filter value list contains only one type of operations.
[中]检查筛选值列表是否仅包含一种类型的操作。

代码示例

代码示例来源：origin: opencb/opencga

protected QueryOperation getQueryOperation(String valuesStr) {
  QueryOperation queryOperation = VariantQueryUtils.checkOperator(valuesStr);
  if (queryOperation == null) {
    queryOperation = QueryOperation.OR;
  }
  return queryOperation;
}

代码示例来源：origin: opencb/opencga

/**
 * Checks that the filter value list contains only one type of operations.
 *
 * @param value List of values to check
 * @return The used operator. Null if no operator is used.
 * @throws VariantQueryException if the list contains different operators.
 */
public static QueryOperation checkOperator(String value) throws VariantQueryException {
  return checkOperator(value, null);
}

代码示例来源：origin: opencb/opencga

private QueryOperation parseOrAndFilter(String param, String value) {
  QueryOperation queryOperation = VariantQueryUtils.checkOperator(value, VariantQueryParam.valueOf(param));
  if (queryOperation == null) {
    // return AND by default
    return QueryOperation.AND;
  } else {
    return queryOperation;
  }
}

代码示例来源：origin: opencb/opencga

/**
 * Splits the string with the specified operation.
 *
 * @param value     Value to split
 * @return List of values, without the delimiter
 */
public static Pair<QueryOperation, List<String>> splitValue(String value) {
  QueryOperation operation = checkOperator(value);
  return Pair.of(operation, splitValue(value, operation));
}

代码示例来源：origin: opencb/opencga

private <T> QueryBuilder addQueryFilter(String key, String value, final QueryBuilder builder, QueryOperation op,
                    Function<String, T> map) {
  VariantQueryUtils.QueryOperation intraOp = checkOperator(value);
  return addQueryFilter(key, splitValue(value, intraOp), builder, op, intraOp, map);
}

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

/**
 * Accept filters separated with "," or ";" with the expression:
 * [{STUDY}:]{COHORT}{OPERATION}{VALUE}.
 * Where STUDY is optional if defaultStudyConfiguration is provided
 *
 * @param key                       Stats field to filter
 * @param values                    Values to parse
 * @param builder                   QueryBuilder
 * @param defaultStudyConfiguration
 */
private void addStatsFilterList(String key, String values, QueryBuilder builder, StudyConfiguration defaultStudyConfiguration) {
  QueryOperation op = checkOperator(values);
  List<String> valuesList = splitValue(values, op);
  List<DBObject> statsQueries = new LinkedList<>();
  for (String value : valuesList) {
    statsQueries.add(addStatsFilter(key, value, new QueryBuilder(), defaultStudyConfiguration).get());
  }
  if (!statsQueries.isEmpty()) {
    if (op == QueryOperation.OR) {
      builder.or(statsQueries.toArray(new DBObject[statsQueries.size()]));
    } else {
      builder.and(statsQueries.toArray(new DBObject[statsQueries.size()]));
    }
  }
}

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

/**
 * Parse INFO param.
 *
 * @param query Query to parse
 * @return a pair with the internal QueryOperation (AND/OR) and a map between Files and INFO filters.
 */
public static Pair<QueryOperation, Map<String, String>> parseInfo(Query query) {
  if (!isValidParam(query, INFO)) {
    return Pair.of(null, Collections.emptyMap());
  }
  String value = query.getString(INFO.key());
  if (value.contains(IS)) {
    return parseMultiKeyValueFilter(INFO, value);
  } else {
    List<String> files = query.getAsStringList(FILE.key());
    files.removeIf(VariantQueryUtils::isNegated);
    if (files.isEmpty()) {
      files = query.getAsStringList(INCLUDE_FILE.key());
    }
    if (files.isEmpty()) {
      throw VariantQueryException.malformedParam(INFO, value, "Missing \"" + FILE.key() + "\" param.");
    }
    QueryOperation operator = checkOperator(value);
    Map<String, String> map = new LinkedHashMap<>(files.size());
    for (String file : files) {
      map.put(file, value);
    }
    return Pair.of(operator, map);
  }
}

代码示例来源：origin: opencb/opencga

public static List<String> getIncludeStudiesList(Query query, Set<VariantField> fields) {
  List<String> studies;
  if (!fields.contains(VariantField.STUDIES)) {
    studies = Collections.emptyList();
  } else if (isValidParam(query, INCLUDE_STUDY)) {
    String includeStudy = query.getString(VariantQueryParam.INCLUDE_STUDY.key());
    if (NONE.equals(includeStudy)) {
      studies = Collections.emptyList();
    } else if (ALL.equals(includeStudy)) {
      studies = null;
    } else {
      studies = query.getAsStringList(VariantQueryParam.INCLUDE_STUDY.key());
    }
  } else if (isValidParam(query, STUDY)) {
    String value = query.getString(VariantQueryParam.STUDY.key());
    studies = new ArrayList<>(splitValue(value, checkOperator(value)));
    studies.removeIf(VariantQueryUtils::isNegated);
    // if empty, all the studies
    if (studies.isEmpty()) {
      studies = null;
    }
  } else {
    studies = null;
  }
  return studies;
}

代码示例来源：origin: opencb/opencga

@Test
public void testCheckOperatorMixQuotesAnd() throws Exception {
  assertEquals(VariantQueryUtils.QueryOperation.AND, VariantQueryUtils.checkOperator("a;\"b,c\""));
}

代码示例来源：origin: opencb/opencga

@Test
public void testCheckOperatorMix() throws Exception {
  thrown.expect(VariantQueryException.class);
  VariantQueryUtils.checkOperator("a,b;c");
}

代码示例来源：origin: opencb/opencga

@Test
public void testCheckOperatorMixQuotesOr() throws Exception {
  assertEquals(VariantQueryUtils.QueryOperation.OR, VariantQueryUtils.checkOperator("a,\"b;c\""));
}

代码示例来源：origin: opencb/opencga

@Test
public void testCheckOperatorOR() throws Exception {
  assertEquals(VariantQueryUtils.QueryOperation.OR, VariantQueryUtils.checkOperator("a,b,c"));
}

代码示例来源：origin: opencb/opencga

@Test
public void testCheckOperatorANY() throws Exception {
  assertNull(VariantQueryUtils.checkOperator("a"));
}

代码示例来源：origin: opencb/opencga

@Test
public void testCheckOperatorAND() throws Exception {
  assertEquals(VariantQueryUtils.QueryOperation.AND, VariantQueryUtils.checkOperator("a;b;c"));
}

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

public static StudyConfiguration getDefaultStudyConfiguration(Query query, QueryOptions options,
                               StudyConfigurationManager studyConfigurationManager) {
  final StudyConfiguration defaultStudyConfiguration;
  if (isValidParam(query, VariantQueryParam.STUDY)) {
    String value = query.getString(VariantQueryParam.STUDY.key());
    // Check that the study exists
    VariantQueryUtils.QueryOperation studiesOperation = checkOperator(value);
    List<String> studiesNames = splitValue(value, studiesOperation);
    List<Integer> studyIds = studyConfigurationManager.getStudyIds(studiesNames, options); // Non negated studyIds
    if (studyIds.size() == 1) {
      defaultStudyConfiguration = studyConfigurationManager.getStudyConfiguration(studyIds.get(0), null).first();
    } else {
      defaultStudyConfiguration = null;
    }
  } else {
    List<String> studyNames = studyConfigurationManager.getStudyNames(null);
    if (studyNames != null && studyNames.size() == 1) {
      defaultStudyConfiguration = studyConfigurationManager.getStudyConfiguration(studyNames.get(0), new QueryOptions()).first();
    } else {
      defaultStudyConfiguration = null;
    }
  }
  return defaultStudyConfiguration;
}

代码示例来源：origin: opencb/opencga

/**
 * Accept a list of comparative filters separated with "," or ";" with the expression:
 * {OPERATION}{VALUE}, where the accepted operations are: <, <=, >, >=, =, ==, !=, ~=.
 *
 * @param key
 * @param value
 * @param builder
 * @param extendKey
 * @return
 */
private QueryBuilder addCompListQueryFilter(String key, String value, QueryBuilder builder, boolean extendKey) {
  VariantQueryUtils.QueryOperation op = checkOperator(value);
  List<String> values = splitValue(value, op);
  QueryBuilder compBuilder;
  if (op == QueryOperation.OR) {
    compBuilder = QueryBuilder.start();
  } else {
    compBuilder = builder;
  }
  for (String elem : values) {
    addCompQueryFilter(key, elem, compBuilder, extendKey);
  }
  if (op == QueryOperation.OR) {
    builder.or(compBuilder.get());
  }
  return builder;
}