Example usage for com.mongodb.client.model Filters in

Introduction

In this page you can find the example usage for com.mongodb.client.model Filters in.

Prototype

public static <TItem> Bson in(final String fieldName, final Iterable<TItem> values)

Source Link

Document

Creates a filter that matches all documents where the value of a field equals any value in the list of specified values.

Usage

From source file:org.opencb.opencga.catalog.db.mongodb.MetaMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult<StudyAclEntry> getDaemonAcl(List<String> members) throws CatalogDBException {
    long startTime = startQuery();

    Bson match = Aggregates.match(Filters.eq(PRIVATE_ID, "METADATA"));
    Bson unwind = Aggregates.unwind("$" + CohortDBAdaptor.QueryParams.ACL.key());
    Bson match2 = Aggregates.match(Filters.in(CohortDBAdaptor.QueryParams.ACL_MEMBER.key(), members));
    Bson project = Aggregates.project(// w w  w.  jav  a 2 s .c  o m
            Projections.include(CohortDBAdaptor.QueryParams.ID.key(), CohortDBAdaptor.QueryParams.ACL.key()));

    QueryResult<Document> aggregate = metaCollection.aggregate(Arrays.asList(match, unwind, match2, project),
            null);
    StudyAclEntry result = null;
    if (aggregate.getNumResults() == 1) {
        result = parseObject(((Document) aggregate.getResult().get(0).get("acl")), StudyAclEntry.class);
    }
    return endQuery("get daemon Acl", startTime, Arrays.asList(result));
}

From source file:org.opencb.opencga.catalog.db.mongodb.MongoDBUtils.java

License:Apache License

static QueryResult<Document> getAcl(long id, List<String> members, MongoDBCollection collection, Logger logger)
        throws CatalogDBException {
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.eq(PRIVATE_ID, id)));
    aggregation.add(Aggregates.project(//ww w .java2  s.c  o m
            Projections.include(FileDBAdaptor.QueryParams.ID.key(), FileDBAdaptor.QueryParams.ACL.key())));
    aggregation.add(Aggregates.unwind("$" + FileDBAdaptor.QueryParams.ACL.key()));

    List<Bson> filters = new ArrayList<>();
    if (members != null && members.size() > 0) {
        filters.add(Filters.in(FileDBAdaptor.QueryParams.ACL_MEMBER.key(), members));
    }

    if (filters.size() > 0) {
        Bson filter = filters.size() == 1 ? filters.get(0) : Filters.and(filters);
        aggregation.add(Aggregates.match(filter));
    }

    for (Bson bson : aggregation) {
        logger.debug("Get Acl: {}",
                bson.toBsonDocument(Document.class, com.mongodb.MongoClient.getDefaultCodecRegistry()));
    }

    return collection.aggregate(aggregation, null);
}

From source file:org.opencb.opencga.catalog.db.mongodb.StudyMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult<Group> getGroup(long studyId, @Nullable String groupId, List<String> userIds)
        throws CatalogDBException {
    long startTime = startQuery();
    checkId(studyId);// w w w.j av a  2 s .  com
    for (String userId : userIds) {
        dbAdaptorFactory.getCatalogUserDBAdaptor().checkId(userId);
    }
    if (groupId != null && groupId.length() > 0 && !groupExists(studyId, groupId)) {
        throw new CatalogDBException("Group \"" + groupId + "\" does not exist in study " + studyId);
    }

    /*
    * List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.elemMatch(QueryParams.VARIABLE_SET.key(),
        Filters.eq(VariableSetParams.ID.key(), variableSetId))));
    aggregation.add(Aggregates.project(Projections.include(QueryParams.VARIABLE_SET.key())));
    aggregation.add(Aggregates.unwind("$" + QueryParams.VARIABLE_SET.key()));
    aggregation.add(Aggregates.match(Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId)));
    QueryResult<VariableSet> queryResult = studyCollection.aggregate(aggregation, variableSetConverter, new QueryOptions());
    * */
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.eq(PRIVATE_ID, studyId)));
    aggregation.add(Aggregates.project(Projections.include(QueryParams.GROUPS.key())));
    aggregation.add(Aggregates.unwind("$" + QueryParams.GROUPS.key()));

    //        Document query = new Document(PRIVATE_ID, studyId);
    //        List<Bson> groupQuery = new ArrayList<>();
    if (userIds.size() > 0) {
        aggregation.add(Aggregates.match(Filters.in(QueryParams.GROUP_USER_IDS.key(), userIds)));
        //            groupQuery.add(Filters.in("userIds", userIds));
    }
    if (groupId != null && groupId.length() > 0) {
        aggregation.add(Aggregates.match(Filters.eq(QueryParams.GROUP_NAME.key(), groupId)));
        //            groupQuery.add(Filters.eq("id", groupId));
    }

    //        Bson projection = new Document(QueryParams.GROUPS.key(), new Document("$elemMatch", groupQuery));

    QueryResult<Document> queryResult = studyCollection.aggregate(aggregation, null);

    //        QueryResult<Document> queryResult = studyCollection.find(query, projection, null);
    List<Study> studies = MongoDBUtils.parseStudies(queryResult);
    List<Group> groups = new ArrayList<>();
    studies.stream().filter(study -> study.getGroups() != null)
            .forEach(study -> groups.addAll(study.getGroups()));
    return endQuery("getGroup", startTime, groups);
}

From source file:org.opencb.opencga.storage.mongodb.variant.adaptors.VariantSourceMongoDBAdaptor.java

License:Apache License

protected Bson parseQuery(Query query) {
    LinkedList<Bson> filters = new LinkedList<>();
    if (query.containsKey(VariantSourceQueryParam.STUDY_ID.key())) {
        List<String> studyIds = query.getAsStringList(VariantSourceQueryParam.STUDY_ID.key());
        filters.add(Filters.in(VariantSourceQueryParam.STUDY_ID.key(), studyIds));
    }/*w  w w.  j a  v a 2  s .c  o m*/
    if (query.containsKey(VariantSourceQueryParam.FILE_ID.key())) {
        List<String> studyIds = query.getAsStringList(VariantSourceQueryParam.FILE_ID.key());
        filters.add(Filters.in(VariantSourceQueryParam.FILE_ID.key(), studyIds));
    }

    return Filters.and(filters);
}