How to use

VariantFileMetadataDBAdaptor$VariantFileMetadataQueryParam

in

org.opencb.opencga.storage.core.metadata.adaptors

protected Bson parseQuery(Query query) {
  LinkedList<Bson> filters = new LinkedList<>();
  if (VariantQueryUtils.isValidParam(query, VariantFileMetadataQueryParam.STUDY_ID)) {
    List<String> studyIds = query.getAsStringList(VariantFileMetadataQueryParam.STUDY_ID.key());
    if (VariantQueryUtils.isValidParam(query, VariantFileMetadataQueryParam.FILE_ID)) {
      List<String> fileIds = query.getAsStringList(VariantFileMetadataQueryParam.FILE_ID.key());
      List<String> ids = new ArrayList<>(studyIds.size() * fileIds.size());
      for (String studyId : studyIds) {
        for (String fileId : fileIds) {
          ids.add(DocumentToVariantFileMetadataConverter.buildId(studyId, fileId));
        }
      }
      filters.add(Filters.in("_id", ids));
    } else {
      for (String studyId : studyIds) {
        filters.add(Filters.regex("_id", '^' + DocumentToVariantFileMetadataConverter.buildId(studyId, "")));
      }
    }
  } else if (query.containsKey(VariantFileMetadataQueryParam.FILE_ID.key())) {
    List<String> fileIds = query.getAsStringList(VariantFileMetadataQueryParam.FILE_ID.key());
    filters.add(Filters.in("id", fileIds));
  }
  if (filters.isEmpty()) {
    return new Document();
  } else {
    return Filters.and(filters);
  }
}

@Override
public QueryResult updateStats(VariantSourceStats variantSourceStats, StudyConfiguration studyConfiguration, QueryOptions
    queryOptions) {
  MongoDBCollection coll = db.getCollection(collectionName);
  VariantFileMetadata source = new VariantFileMetadata("", "");
  source.setStats(variantSourceStats.getFileStats());
  Document globalStats = variantFileMetadataConverter.convertToStorageType("", source).get("stats", Document.class);
  Bson query = parseQuery(new Query(VariantFileMetadataQueryParam.STUDY_ID.key(), variantSourceStats.getStudyId())
      .append(VariantFileMetadataQueryParam.FILE_ID.key(), variantSourceStats.getFileId()));
  Bson update = Updates.set("stats", globalStats);
  return coll.update(query, update, null);
}

@Override
public Iterator<VariantFileMetadata> iterator(Query query, QueryOptions options) throws IOException {
  int studyId = query.getInt(VariantFileMetadataQueryParam.STUDY_ID.key());
  List<Integer> fileIds = query.getAsIntegerList(VariantFileMetadataQueryParam.FILE_ID.key());
  return iterator(studyId, fileIds, options);
}

default QueryResult<VariantFileMetadata> get(int studyId, int fileId, QueryOptions options) throws StorageEngineException {
  StopWatch stopWatch = StopWatch.createStarted();
  Iterator<VariantFileMetadata> iterator;
  try {
    Query query = new Query(VariantFileMetadataQueryParam.FILE_ID.key(), fileId)
        .append(VariantFileMetadataQueryParam.STUDY_ID.key(), studyId);
    iterator = iterator(query, options);
  } catch (IOException e) {
    throw new StorageEngineException("Error reading from VariantFileMetadataDBAdaptor", e);
  }
  VariantFileMetadata metadata = Iterators.getOnlyElement(iterator, null);
  if (metadata != null) {
    return new QueryResult<>("", ((int) stopWatch.getTime(TimeUnit.MILLISECONDS)), 1, 1, null, null,
        Collections.singletonList(metadata));
  } else {
    return new QueryResult<>("", ((int) stopWatch.getTime(TimeUnit.MILLISECONDS)), 0, 0, null, null, Collections.emptyList());
  }
}

protected VariantMetadata makeVariantMetadata(List<StudyConfiguration> studyConfigurations,
                       ProjectMetadata projectMetadata, Map<Integer, List<Integer>> returnedSamples,
                       Map<Integer, List<Integer>> returnedFiles, QueryOptions queryOptions)
    throws StorageEngineException {
  VariantMetadata metadata = new VariantMetadataConverter()
      .toVariantMetadata(studyConfigurations, projectMetadata, returnedSamples, returnedFiles);
  Map<String, StudyConfiguration> studyConfigurationMap = studyConfigurations.stream()
      .collect(Collectors.toMap(StudyConfiguration::getStudyName, Function.identity()));
  for (VariantStudyMetadata studyMetadata : metadata.getStudies()) {
    StudyConfiguration studyConfiguration = studyConfigurationMap.get(studyMetadata.getId());
    List<Integer> fileIds = studyMetadata.getFiles().stream()
        .map(fileMetadata -> {
          Integer fileId = studyConfiguration.getFileIds().get(fileMetadata.getId());
          if (fileId == null) {
            fileId = studyConfiguration.getFileIds().get(fileMetadata.getPath());
          }
          return fileId;
        }).collect(Collectors.toList());
    if (fileIds != null && !fileIds.isEmpty()) {
      Query query = new Query()
          .append(VariantFileMetadataDBAdaptor.VariantFileMetadataQueryParam.STUDY_ID.key(), studyConfiguration.getStudyId())
          .append(VariantFileMetadataDBAdaptor.VariantFileMetadataQueryParam.FILE_ID.key(), fileIds);
      scm.variantFileMetadataIterator(query, new QueryOptions()).forEachRemaining(fileMetadata -> {
        studyMetadata.getFiles().removeIf(file -> file.getId().equals(fileMetadata.getId()));
        studyMetadata.getFiles().add(fileMetadata.getImpl());
      });
    }
  }
  return metadata;
}

.append(VariantFileMetadataDBAdaptor.VariantFileMetadataQueryParam.STUDY_ID.key(), studyConfiguration.getStudyId())
.append(VariantFileMetadataDBAdaptor.VariantFileMetadataQueryParam.FILE_ID.key(), fileId);