org.molgenis.data.support.QueryImpl类的使用及代码示例

x33g5p2x  于2022-01-28 转载在 其他  
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本文整理了Java中org.molgenis.data.support.QueryImpl类的一些代码示例，展示了QueryImpl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。QueryImpl类的具体详情如下：
包路径：org.molgenis.data.support.QueryImpl
类名称：QueryImpl

QueryImpl介绍

暂无

代码示例

代码示例来源：origin: org.molgenis/molgenis-genomebrowser

private Stream<GenomeBrowserAttributes> getDefaultGenomeBrowserAttributes() {
 return dataService.findAll(
   GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES,
   new QueryImpl<GenomeBrowserAttributes>().eq(GenomeBrowserAttributesMetadata.DEFAULT, true),
   GenomeBrowserAttributes.class);
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

public List<String> searchAllOntologies()
{
  List<String> ontologyUris = new ArrayList<String>();
  SearchResult result = searchService.search(new SearchRequest(null, new QueryImpl().pageSize(Integer.MAX_VALUE)
      .eq(OntologyTermIndexRepository.ENTITY_TYPE, OntologyIndexRepository.TYPE_ONTOLOGY), null));
  for (Hit hit : result.getSearchHits())
  {
    Map<String, Object> columnValueMap = hit.getColumnValueMap();
    if (columnValueMap.containsKey("url")) ontologyUris.add(AsyncOntologyIndexer
        .createOntologyTermDocumentType(columnValueMap.get("url").toString()));
  }
  return ontologyUris;
}

代码示例来源：origin: org.molgenis/molgenis-ontology-core

public List<OntologyTerm> findOntologyTerms(String term, int pageSize) {
 Iterable<Entity> ontologyTermEntities;
 // #1 find exact match
 Query<Entity> termNameQuery =
   new QueryImpl<>().eq(OntologyTermMetaData.ONTOLOGY_TERM_NAME, term).pageSize(pageSize);
 ontologyTermEntities = () -> dataService.findAll(ONTOLOGY_TERM, termNameQuery).iterator();
 if (!ontologyTermEntities.iterator().hasNext()) {
  Query<Entity> termsQuery = new QueryImpl<>().search(term).pageSize(pageSize);
  ontologyTermEntities = () -> dataService.findAll(ONTOLOGY_TERM, termsQuery).iterator();
 }
 return Lists.newArrayList(
   Iterables.transform(ontologyTermEntities, OntologyTermRepository::toOntologyTerm));
}

代码示例来源：origin: org.molgenis/molgenis-data-index

/**
 * Retrieves all {@link EntityType}s. Queryies in pages of size ENTITY_FETCH_PAGE_SIZE so that
 * results can be cached. Uses a {@link Fetch} that specifies all fields needed to determine the
 * necessary index actions.
 *
 * @return List containing all {@link EntityType}s.
 */
private List<EntityType> getEntityTypes() {
 QueryImpl<EntityType> query = new QueryImpl<>();
 query.setPageSize(ENTITY_FETCH_PAGE_SIZE);
 query.setFetch(ENTITY_TYPE_FETCH);
 List<EntityType> result = newArrayList();
 for (int pageNum = 0; result.size() == pageNum * ENTITY_FETCH_PAGE_SIZE; pageNum++) {
  query.offset(pageNum * ENTITY_FETCH_PAGE_SIZE);
  dataService.findAll(ENTITY_TYPE_META_DATA, query, EntityType.class).forEach(result::add);
 }
 return result;
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

public StoreMappingRepository(DataSet dataSet, DataService dataService)
{
  super("mapping://" + dataSet.getIdentifier());
  this.dataSet = dataSet;
  Iterable<ObservationSet> observationSets = dataService.findAll(ObservationSet.ENTITY_NAME,
      new QueryImpl().eq(ObservationSet.PARTOFDATASET, dataSet), ObservationSet.class);
  observedValues = dataService.findAll(ObservedValue.ENTITY_NAME,
      new QueryImpl().in(ObservedValue.OBSERVATIONSET, Lists.newArrayList(observationSets)),
      ObservedValue.class);
  valueConverter = new ValueConverter(dataService);
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

QueryImpl q = new QueryImpl();
q.pageSize(Integer.MAX_VALUE);
q.addRule(new QueryRule(PROTOCOLTREE_TYPE_FIELD, Operator.EQUALS, ObservableFeature.ENTITY_NAME.toLowerCase()));
      new QueryImpl().in(ObservableFeature.ID, listOfFeatureIds), ObservableFeature.class);
  for (ObservableFeature feature : features)

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

@Override
public Query query()
{
  return new QueryImpl(this);
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

public Set<String> findOntologyTermSynonyms(Hit ontologyTermHit)
{
  String ontologyTermIRI = ontologyTermHit.getColumnValueMap().get(ONTOLOGY_TERM_IRI).toString();
  Set<String> synonyms = new HashSet<String>();
  QueryImpl query = new QueryImpl();
  query.addRule(new QueryRule(ONTOLOGY_TERM_IRI, Operator.EQUALS, ontologyTermIRI));
  query.pageSize(100000);
  SearchRequest searchRequest = new SearchRequest(null, query, null);
  SearchResult searchResult = searchService.search(searchRequest);
  for (Hit hit : searchResult.getSearchHits())
  {
    synonyms.add(hit.getColumnValueMap().get(ONTOLOGYTERM_SYNONYM).toString().toLowerCase());
  }
  return synonyms;
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

public SearchResult findOntologyTerm(List<String> queryStrings)
{
  QueryImpl query = new QueryImpl();
  if (queryStrings.size() > 0)
  {
    for (String queryString : queryStrings)
    {
      if (query.getRules().size() > 0) query.addRule(new QueryRule(Operator.OR));
      query.addRule(new QueryRule(ONTOLOGYTERM_SYNONYM, Operator.EQUALS, queryString));
    }
    query.addRule(new QueryRule(Operator.AND));
    query.addRule(new QueryRule(ENTITY_TYPE, Operator.EQUALS, "ontologyTerm"));
    query.pageSize(100);
  }
  return searchService.search(new SearchRequest(null, query, null));
}

代码示例来源：origin: org.molgenis/molgenis-model-registry

Query<Package> packageQuery = new QueryImpl<Package>().search(searchTerm);
dataService.findAll(PACKAGE, packageQuery, Package.class).forEach(packageEntity ->
Query<EntityType> entityTypeQuery = new QueryImpl<EntityType>().search(searchTerm);

代码示例来源：origin: org.molgenis/molgenis-data-rest

public Query<Entity> parseQueryString(Map<String, String[]> parameterMap) {
  QueryImpl<Entity> q = new QueryImpl<>();

  for (Map.Entry<String, String[]> entry : parameterMap.entrySet()) {
   String paramName = entry.getKey();
   String[] paramValues = entry.getValue();

   if ((paramValues != null) && (paramValues.length > 0) && (paramValues[0] != null)) {
    if (paramName.equalsIgnoreCase("num")) {
     q.pageSize(DataConverter.toInt(paramValues[0]));
    } else if (paramName.equalsIgnoreCase("start")) {
     q.offset(DataConverter.toInt(paramValues[0]));
    } else if (paramName.equalsIgnoreCase("q")) {
     Query<Entity> query = molgenisRSQL.createQuery(paramValues[0], entityType);
     for (QueryRule rule : query.getRules()) {
      q.addRule(rule);
     }
    }
   }
  }

  return q;
 }
}

代码示例来源：origin: org.molgenis/molgenis-data-mapper

Long num = mappingServiceRequest.getNum();
Query<Entity> query = new QueryImpl<>().offset(offset.intValue()).pageSize(num.intValue());
String sourceEntityName = mappingServiceRequest.getSourceEntityName();
Iterable<Entity> sourceEntities = () -> dataService.findAll(sourceEntityName, query).iterator();
long total = dataService.count(sourceEntityName, new QueryImpl<>());
long nrSuccess = 0, nrErrors = 0;

代码示例来源：origin: org.molgenis/molgenis-data-rest

new QueryImpl<>(queryRules)
    .pageSize(request.getNum())
    .offset(request.getStart())
    .sort(sort);
Long count = repository.count(new QueryImpl<>(q).setOffset(0).setPageSize(0));
EntityPager pager = new EntityPager(request.getStart(), request.getNum(), count, it);

代码示例来源：origin: org.molgenis/molgenis-web

case "=notlike=":
 String notLikeValue = values.get(0);
 q.not().like(attrName, notLikeValue);
 break;
case "=q=":
 String searchValue = values.get(0);
 if (attrName.equals("*")) {
  q.search(searchValue);
 } else {
  q.search(attrName, searchValue);
 q.eq(attrName, eqValue);
 break;
case "=in=":
 Attribute inAttr = getAttribute(node);
 q.in(
   attrName,
   values.stream().map(value -> rsqlValueParser.parse(value, inAttr)).collect(toList()));
 validateNumericOrDate(ltAttr);
 Object ltValue = rsqlValueParser.parse(values.get(0), ltAttr);
 q.lt(attrName, ltValue);
 break;
case "=le=":
 validateNumericOrDate(leAttr);
 Object leValue = rsqlValueParser.parse(values.get(0), leAttr);
 q.le(attrName, leValue);
 break;

代码示例来源：origin: org.molgenis/molgenis-data-index

/** Retrieves the query to get all index actions sorted */
static Query<IndexAction> createQueryGetAllIndexActions(String transactionId) {
 QueryRule rule = new QueryRule(INDEX_ACTION_GROUP_ATTR, EQUALS, transactionId);
 QueryImpl<IndexAction> q = new QueryImpl<>(rule);
 q.setSort(new Sort(ACTION_ORDER));
 return q;
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

private List<Hit> findOntologyTerms(Hit candidateFeature)
{
  Integer featureId = Integer.parseInt(candidateFeature.getColumnValueMap()
      .get(ObservableFeature.ID.toLowerCase()).toString());
  ObservableFeature feature = dataService.findOne(ObservableFeature.ENTITY_NAME, featureId,
      ObservableFeature.class);
  QueryImpl query = new QueryImpl();
  for (OntologyTerm ot : feature.getDefinitions())
  {
    if (query.getRules().size() > 0) query.addRule(new QueryRule(Operator.OR));
    query.addRule(new QueryRule(ONTOLOGY_TERM_IRI, Operator.EQUALS, ot.getTermAccession()));
  }
  return searchService.search(new SearchRequest(null, query, null)).getSearchHits();
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

QueryImpl q = new QueryImpl();
q.pageSize(SIZE_OF_ANNOTATION);
      q.addRule(new QueryRule(Operator.OR));
    q.addRule(new QueryRule(OntologyTermIndexRepository.SYNONYMS, Operator.SEARCH, term));
    first = false;
      new QueryImpl().in(OntologyTerm.IDENTIFIER, new ArrayList<String>(mapUriTerm.keySet())),
      OntologyTerm.class);
      new QueryImpl().eq(Ontology.IDENTIFIER, ontologyUri), Ontology.class);
    new QueryImpl().in(OntologyTerm.IDENTIFIER, identifiers), OntologyTerm.class);

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

@Override
public Query query()
{
  return new QueryImpl(this);
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

private SearchResult findAllFeatures(Integer targetDataSetId)
{
  QueryImpl query = new QueryImpl();
  query.addRule(new QueryRule(ENTITY_TYPE, Operator.EQUALS, ObservableFeature.class.getSimpleName().toLowerCase()));
  query.pageSize(1000000);
  DataSet dataSet = dataService.findOne(DataSet.ENTITY_NAME, targetDataSetId, DataSet.class);
  return searchService
      .search(new SearchRequest(CATALOGUE_PREFIX + dataSet.getProtocolUsed().getId(), query, null));
}

代码示例来源：origin: org.molgenis/molgenis-omx-biobankconnect

public String validateAlgorithmInputs(Integer dataSetId, String algorithm)
{
  if (StringUtils.isEmpty(algorithm))
  {
    return ("Algorithm is not defined!");
  }
  Iterable<ObservableFeature> featureIterators = dataService.findAll(ObservableFeature.ENTITY_NAME,
      new QueryImpl().in(ObservableFeature.NAME, extractFeatureName(algorithm)), ObservableFeature.class);
  if (Iterables.size(featureIterators) == 0)
  {
    return ("Variables are not found! Please check the name of variables!");
  }
  DataSet sourceDataSet = dataService.findOne(DataSet.ENTITY_NAME, dataSetId, DataSet.class);
  Iterable<ObservationSet> observationSets = dataService.findAll(ObservationSet.ENTITY_NAME,
      new QueryImpl().eq(ObservationSet.PARTOFDATASET, sourceDataSet), ObservationSet.class);
  if (Iterables.size(observationSets) == 0)
  {
    return ("There are not rows in this dataset!");
  }
  return StringUtils.EMPTY;
}

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