org.opencb.cellbase.mongodb.db.MutationMongoDBAdaptor.java Source code

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Here is the source code for org.opencb.cellbase.mongodb.db.MutationMongoDBAdaptor.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.mongodb.db;

import com.mongodb.*;
import org.opencb.biodata.models.feature.Region;
import org.opencb.cellbase.core.common.Position;
import org.opencb.cellbase.core.lib.api.variation.MutationDBAdaptor;
import org.opencb.datastore.core.QueryOptions;
import org.opencb.datastore.core.QueryResult;
import org.opencb.datastore.mongodb.MongoDataStore;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Created with IntelliJ IDEA.
 * User: imedina
 * Date: 25/11/13
 * Time: 14:04
 * To change this template use File | Settings | File Templates.
 */
@Deprecated
public class MutationMongoDBAdaptor extends MongoDBAdaptor implements MutationDBAdaptor {

    public MutationMongoDBAdaptor(DB db, String species, String version) {
        super(db, species, version);
        mongoDBCollection = db.getCollection("mutation");
    }

    public MutationMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) {
        super(species, assembly, mongoDataStore);
        mongoDBCollection = db.getCollection("mutation");
        mongoDBCollection2 = mongoDataStore.getCollection("mutation");

        logger.info("MutationMongoDBAdaptor: in 'constructor'");
    }

    @Override
    public QueryResult getAll(QueryOptions options) {
        QueryBuilder builder = new QueryBuilder();

        List<Object> biotypes = options.getList("disease", null);
        if (biotypes != null && biotypes.size() > 0) {
            BasicDBList biotypeIds = new BasicDBList();
            biotypeIds.addAll(biotypes);
            builder = builder.and("primaryHistology").in(biotypeIds);
        }

        return executeQuery("result", builder.get(), options);
    }

    @Override
    public QueryResult getAllById(String id, QueryOptions options) {
        return getAllByIdList(Arrays.asList(id), options).get(0);
    }

    @Override
    public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>(idList.size());
        for (String id : idList) {
            QueryBuilder builder = QueryBuilder.start("id").is(id);
            queries.add(builder.get());
        }

        return executeQueryList(idList, queries, options);
    }

    @Override
    public QueryResult getAllDiseases(QueryOptions options) {
        //        List<String> diseases = mongoDBCollection.distinct("primaryHistology");
        //        DBObject distinct = new BasicDBObject("distinct", "primaryHistology");
        //        System.out.println(distinct.toString());
        //        return executeDistinct("distinct", "primaryHistology");
        return null;
    }

    @Override
    public QueryResult getAllByDisease(String id, QueryOptions options) {
        return getAllByDiseaseList(Arrays.asList(id), options).get(0);
    }

    @Override
    public List<QueryResult> getAllByDiseaseList(List<String> idList, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>(idList.size());
        for (String id : idList) {
            QueryBuilder builder = QueryBuilder.start("primaryHistology").is(id);
            queries.add(builder.get());
        }

        return executeQueryList(idList, queries, options);
    }

    @Override
    public QueryResult getByGeneName(String geneName, QueryOptions options) {
        return getAllByIdList(Arrays.asList(geneName), options).get(0);
    }

    @Override
    public List<QueryResult> getAllByGeneNameList(List<String> geneNameList, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>();
        for (String id : geneNameList) {
            QueryBuilder builder = QueryBuilder.start("gene").is(id);
            queries.add(builder.get());
        }

        return executeQueryList(geneNameList, queries, options);
    }

    @Override
    public QueryResult getByProteinId(String proteinId, QueryOptions options) {
        return getAllByIdList(Arrays.asList(proteinId), options).get(0);
    }

    @Override
    public List<QueryResult> getAllByProteinIdList(List<String> proteinIdList, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>();
        for (String id : proteinIdList) {
            QueryBuilder builder = QueryBuilder.start("protein").is(id);
            queries.add(builder.get());
        }

        return executeQueryList(proteinIdList, queries, options);
    }

    @Override
    public QueryResult getByProteinRegion(String proteinId, int start, int end, QueryOptions options) {
        return null; //To change body of implemented methods use File | Settings | File Templates.
    }

    @Override
    public QueryResult getAllByPosition(String chromosome, int position, QueryOptions options) {
        return getAllByRegion(chromosome, position, position, options);
    }

    @Override
    public QueryResult getAllByPosition(Position position, QueryOptions options) {
        return getAllByRegion(new Region(position.getChromosome(), position.getPosition(), position.getPosition()),
                options);
    }

    @Override
    public List<QueryResult> getAllByPositionList(List<Position> positionList, QueryOptions options) {
        List<Region> regions = new ArrayList<>();
        for (Position position : positionList) {
            regions.add(new Region(position.getChromosome(), position.getPosition(), position.getPosition()));
        }
        return getAllByRegionList(regions, options);
    }

    @Override
    public QueryResult getAllByRegion(String chromosome, int start, int end, QueryOptions options) {
        return getAllByRegion(new Region(chromosome, start, end), options);
    }

    @Override
    public QueryResult getAllByRegion(Region region, QueryOptions options) {
        return getAllByRegionList(Arrays.asList(region), options).get(0);
    }

    @Override
    public List<QueryResult> getAllByRegionList(List<Region> regions, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>();

        List<String> ids = new ArrayList<>(regions.size());
        for (Region region : regions) {
            QueryBuilder builder = QueryBuilder.start("chromosome").is(region.getChromosome()).and("start")
                    .greaterThanEquals(region.getStart()).lessThanEquals(region.getEnd());
            queries.add(builder.get());
            ids.add(region.toString());
        }

        return executeQueryList(ids, queries, options);
    }

    @Override
    public QueryResult next(String chromosome, int position, QueryOptions options) {
        return null;
    }

}