How to use

FileAclEntry$FilePermissions

in

org.opencb.opencga.core.models.acls.permissions

public FileAclEntry(String member, ObjectMap permissions) {
  super(member, EnumSet.noneOf(FilePermissions.class));
  EnumSet<FilePermissions> aux = EnumSet.allOf(FilePermissions.class);
  for (FilePermissions permission : aux) {
    if (permissions.containsKey(permission.name()) && permissions.getBoolean(permission.name())) {
      this.permissions.add(permission);
    }
  }
}

    .map(DatasetAclEntry.DatasetPermissions::toString)
    .collect(Collectors.toList()));
this.fullPermissionsMap.put(Entity.FILE, Arrays.stream(FileAclEntry.FilePermissions.values())
    .map(FileAclEntry.FilePermissions::toString)
    .collect(Collectors.toList()));

@Override
public DBIterator<File> iterator(Query query, QueryOptions options, String user)
    throws CatalogDBException, CatalogAuthorizationException {
  Document studyDocument = getStudyDocument(query);
  MongoCursor<Document> mongoCursor = getMongoCursor(query, options, studyDocument, user);
  Function<Document, Document> iteratorFilter = (d) ->  filterAnnotationSets(studyDocument, d, user,
      StudyAclEntry.StudyPermissions.VIEW_FILE_ANNOTATIONS.name(),
      FileAclEntry.FilePermissions.VIEW_ANNOTATIONS.name());
  return new FileMongoDBIterator<>(mongoCursor, fileConverter, iteratorFilter, dbAdaptorFactory.getCatalogSampleDBAdaptor(),
      query.getLong(PRIVATE_STUDY_ID), user, options);
}

@Override
public DBIterator nativeIterator(Query query, QueryOptions options, String user)
    throws CatalogDBException, CatalogAuthorizationException {
  QueryOptions queryOptions = options != null ? new QueryOptions(options) : new QueryOptions();
  queryOptions.put(NATIVE_QUERY, true);
  Document studyDocument = getStudyDocument(query);
  MongoCursor<Document> mongoCursor = getMongoCursor(query, queryOptions, studyDocument, user);
  Function<Document, Document> iteratorFilter = (d) ->  filterAnnotationSets(studyDocument, d, user,
      StudyAclEntry.StudyPermissions.VIEW_FILE_ANNOTATIONS.name(),
      FileAclEntry.FilePermissions.VIEW_ANNOTATIONS.name());
  return new FileMongoDBIterator<>(mongoCursor, null, iteratorFilter, dbAdaptorFactory.getCatalogSampleDBAdaptor(),
      query.getLong(PRIVATE_STUDY_ID), user, options);
}

@Override
public QueryResult groupBy(Query query, List<String> fields, QueryOptions options, String user)
    throws CatalogDBException, CatalogAuthorizationException {
  Document studyDocument = getStudyDocument(query);
  Document queryForAuthorisedEntries;
  if (containsAnnotationQuery(query)) {
    queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user,
        StudyAclEntry.StudyPermissions.VIEW_FILE_ANNOTATIONS.name(),
        FileAclEntry.FilePermissions.VIEW_ANNOTATIONS.name(), Entity.FILE.name());
  } else {
    queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user,
        StudyAclEntry.StudyPermissions.VIEW_FILES.name(), FileAclEntry.FilePermissions.VIEW.name(), Entity.FILE.name());
  }
  filterOutDeleted(query);
  Bson bsonQuery = parseQuery(query, false, queryForAuthorisedEntries);
  return groupBy(fileCollection, bsonQuery, fields, QueryParams.NAME.key(), options);
}

public FileAclEntry.FilePermissions getFilePermission() {
  if (this.type == FILE) {
    return FileAclEntry.FilePermissions.valueOf(this.permission);
  }
  return null;
}

@Override
public QueryResult<Long> count(final Query query, final String user, final StudyAclEntry.StudyPermissions studyPermissions)
    throws CatalogDBException, CatalogAuthorizationException {
  filterOutDeleted(query);
  StudyAclEntry.StudyPermissions studyPermission = (studyPermissions == null
      ? StudyAclEntry.StudyPermissions.VIEW_FILES : studyPermissions);
  // Get the study document
  Query studyQuery = new Query(StudyDBAdaptor.QueryParams.UID.key(), query.getLong(QueryParams.STUDY_UID.key()));
  QueryResult queryResult = dbAdaptorFactory.getCatalogStudyDBAdaptor().nativeGet(studyQuery, QueryOptions.empty());
  if (queryResult.getNumResults() == 0) {
    throw new CatalogDBException("Study " + query.getLong(QueryParams.STUDY_UID.key()) + " not found");
  }
  // Get the document query needed to check the permissions as well
  Document queryForAuthorisedEntries = getQueryForAuthorisedEntries((Document) queryResult.first(), user,
      studyPermission.name(), studyPermission.getFilePermission().name(), Entity.FILE.name());
  Bson bson = parseQuery(query, false, queryForAuthorisedEntries);
  logger.debug("File count: query : {}, dbTime: {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
  return fileCollection.count(bson);
}

private MongoCursor<Document> getMongoCursor(Query query, QueryOptions options, Document studyDocument, String user)
    throws CatalogDBException, CatalogAuthorizationException {
  Document queryForAuthorisedEntries = null;
  if (studyDocument != null && user != null) {
    // Get the document query needed to check the permissions as well
    queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user,
        StudyAclEntry.StudyPermissions.VIEW_FILES.name(), FileAclEntry.FilePermissions.VIEW.name(), Entity.FILE.name());
  }
  filterOutDeleted(query);
  Bson bson = parseQuery(query, false, queryForAuthorisedEntries);
  QueryOptions qOptions;
  if (options != null) {
    qOptions = new QueryOptions(options);
  } else {
    qOptions = new QueryOptions();
  }
  qOptions = removeInnerProjections(qOptions, QueryParams.SAMPLES.key());
  qOptions = removeAnnotationProjectionOptions(qOptions);
  qOptions = filterOptions(qOptions, FILTER_ROUTE_FILES);
  logger.debug("File query: {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry()));
  return fileCollection.nativeQuery().find(bson, qOptions).iterator();
}

    new File.FileStatus(File.FileStatus.STAGE), 1000, 1);
LinkedList<FileAclEntry> acl = new LinkedList<>();
acl.push(new FileAclEntry("jcoll", Arrays.asList(FileAclEntry.FilePermissions.VIEW.name(),
    FileAclEntry.FilePermissions.VIEW_CONTENT.name(), FileAclEntry.FilePermissions.VIEW_HEADER.name(),
    FileAclEntry.FilePermissions.DELETE.name())));
acl.push(new FileAclEntry("jmmut", Collections.emptyList()));
System.out.println(catalogFileDBAdaptor.insert(studyId, file, null, null));

    break;
  default:
    throw new CatalogAuthorizationException("Permission " + permission.toString() + " not found");
  return;
throw CatalogAuthorizationException.deny(userId, permission.toString(), "File", fileId, null);

@Override
public QueryResult groupBy(Query query, String field, QueryOptions options, String user)
    throws CatalogDBException, CatalogAuthorizationException {
  Document studyDocument = getStudyDocument(query);
  Document queryForAuthorisedEntries;
  if (containsAnnotationQuery(query)) {
    queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user,
        StudyAclEntry.StudyPermissions.VIEW_FILE_ANNOTATIONS.name(),
        FileAclEntry.FilePermissions.VIEW_ANNOTATIONS.name(), Entity.FILE.name());
  } else {
    queryForAuthorisedEntries = getQueryForAuthorisedEntries(studyDocument, user,
        StudyAclEntry.StudyPermissions.VIEW_FILES.name(), FileAclEntry.FilePermissions.VIEW.name(), Entity.FILE.name());
  }
  filterOutDeleted(query);
  Bson bsonQuery = parseQuery(query, false, queryForAuthorisedEntries);
  return groupBy(fileCollection, bsonQuery, field, QueryParams.NAME.key(), options);
}