org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor.java Source code

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Here is the source code for org.opencb.cellbase.lib.impl.RegulationMongoDBAdaptor.java

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/*
 * Copyright 2015 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.cellbase.lib.impl;

import com.mongodb.client.model.Filters;
import org.bson.Document;
import org.bson.conversions.Bson;
import org.opencb.biodata.models.core.Region;
import org.opencb.biodata.models.core.RegulatoryFeature;
import org.opencb.cellbase.core.api.RegulationDBAdaptor;
import org.opencb.cellbase.lib.MongoDBCollectionConfiguration;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryResult;
import org.opencb.commons.datastore.mongodb.MongoDataStore;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.function.Consumer;

/**
 * Created by imedina on 07/12/15.
 */
public class RegulationMongoDBAdaptor extends MongoDBAdaptor implements RegulationDBAdaptor<RegulatoryFeature> {

    public RegulationMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) {
        super(species, assembly, mongoDataStore);
        mongoDBCollection = mongoDataStore.getCollection("regulatory_region");

        logger.debug("RegulationMongoDBAdaptor: in 'constructor'");
    }

    @Override
    public QueryResult<RegulatoryFeature> next(Query query, QueryOptions options) {
        return null;
    }

    @Override
    public QueryResult nativeNext(Query query, QueryOptions options) {
        return null;
    }

    @Override
    public QueryResult rank(Query query, String field, int numResults, boolean asc) {
        return null;
    }

    @Override
    public QueryResult groupBy(Query query, String field, QueryOptions options) {
        Bson bsonQuery = parseQuery(query);
        return groupBy(bsonQuery, field, "name", options);
    }

    @Override
    public QueryResult groupBy(Query query, List<String> fields, QueryOptions options) {
        Bson bsonQuery = parseQuery(query);
        return groupBy(bsonQuery, fields, "name", options);
    }

    @Override
    public QueryResult getIntervalFrequencies(Query query, int intervalSize, QueryOptions options) {
        if (query.getString(QueryParams.REGION.key()) != null) {
            Region region = Region.parseRegion(query.getString(QueryParams.REGION.key()));
            Bson bsonDocument = parseQuery(query);
            return getIntervalFrequencies(bsonDocument, region, intervalSize, options);
        }
        return null;
    }

    @Override
    public QueryResult<Long> update(List objectList, String field, String[] innerFields) {
        return null;
    }

    @Override
    public QueryResult<Long> count(Query query) {
        Bson bsonDocument = parseQuery(query);
        return mongoDBCollection.count(bsonDocument);
    }

    @Override
    public QueryResult distinct(Query query, String field) {
        Bson bsonDocument = parseQuery(query);
        return mongoDBCollection.distinct(field, bsonDocument);
    }

    @Override
    public QueryResult stats(Query query) {
        return null;
    }

    @Override
    public QueryResult<RegulatoryFeature> get(Query query, QueryOptions options) {
        Bson bson = parseQuery(query);
        options = addPrivateExcludeOptions(options);
        return mongoDBCollection.find(bson, null, RegulatoryFeature.class, options);
    }

    @Override
    public QueryResult nativeGet(Query query, QueryOptions options) {
        Bson bson = parseQuery(query);
        return mongoDBCollection.find(bson, options);
    }

    @Override
    public Iterator<RegulatoryFeature> iterator(Query query, QueryOptions options) {
        return null;
    }

    @Override
    public Iterator nativeIterator(Query query, QueryOptions options) {
        Bson bson = parseQuery(query);
        return mongoDBCollection.nativeQuery().find(bson, options).iterator();
    }

    @Override
    public void forEach(Query query, Consumer<? super Object> action, QueryOptions options) {

    }

    private Bson parseQuery(Query query) {
        List<Bson> andBsonList = new ArrayList<>();
        createRegionQuery(query, QueryParams.REGION.key(),
                MongoDBCollectionConfiguration.REGULATORY_REGION_CHUNK_SIZE, andBsonList);

        createOrQuery(query, QueryParams.NAME.key(), "name", andBsonList);
        createOrQuery(query, QueryParams.FEATURE_TYPE.key(), "featureType", andBsonList);
        createOrQuery(query, QueryParams.FEATURE_CLASS.key(), "featureClass", andBsonList);
        createOrQuery(query, QueryParams.CELL_TYPES.key(), "cellTypes", andBsonList);
        createOrQuery(query, QueryParams.SCORE.key(), "score", andBsonList);

        if (andBsonList.size() > 0) {
            return Filters.and(andBsonList);
        } else {
            return new Document();
        }
    }
}