org.opencb.cellbase.lib.managers.GenomeManager Maven / Gradle / Ivy

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/*
 * Copyright 2015-2020 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.managers;

import com.google.common.base.Splitter;
import org.opencb.biodata.models.core.*;
import org.opencb.biodata.models.variant.avro.Cytoband;
import org.opencb.biodata.models.variant.avro.Score;
import org.opencb.cellbase.core.ParamConstants;
import org.opencb.cellbase.core.api.GenomeQuery;
import org.opencb.cellbase.core.api.query.CellBaseQueryOptions;
import org.opencb.cellbase.core.config.CellBaseConfiguration;
import org.opencb.cellbase.core.exception.CellBaseException;
import org.opencb.cellbase.core.result.CellBaseDataResult;
import org.opencb.cellbase.lib.impl.core.CellBaseCoreDBAdaptor;
import org.opencb.cellbase.lib.impl.core.GenomeMongoDBAdaptor;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;

import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

public class GenomeManager extends AbstractManager implements AggregationApi {

    private GenomeMongoDBAdaptor genomeDBAdaptor;

    public GenomeManager(String species, CellBaseConfiguration configuration) throws CellBaseException {
        this(species, null, configuration);
    }

    public GenomeManager(String species, String assembly, CellBaseConfiguration configuration)
            throws CellBaseException {
        super(species, assembly, configuration);

        this.init();
    }

    private void init() {
        genomeDBAdaptor = dbAdaptorFactory.getGenomeDBAdaptor();
    }

    @Override
    public CellBaseCoreDBAdaptor getDBAdaptor() {
        return genomeDBAdaptor;
    }


    public CellBaseDataResult getGenomeInfo(QueryOptions queryOptions, int dataRelease) throws CellBaseException {
        return genomeDBAdaptor.getGenomeInfo(queryOptions, dataRelease);
    }

    public List getChromosomes(QueryOptions queryOptions, String chromosomeId, int dataRelease)
            throws CellBaseException {
        List chromosomeList = Splitter.on(",").splitToList(chromosomeId);
        List queryResults = new ArrayList<>(chromosomeList.size());
        for (String chromosome : chromosomeList) {
            CellBaseDataResult queryResult = genomeDBAdaptor.getChromosomeInfo(chromosome, queryOptions, dataRelease);
            queryResult.setId(chromosome);
            queryResults.add(queryResult);
        }
        return queryResults;
    }

    /**
     * For a single query, return the sequence for each region provided. Each region will be its own CellBaseDataResult.
     *
     * @param query The genome query. Should have regions populated
     * @return sequence for each region
     * @throws CellBaseException CellBase exception
     */
    public List> getByRegions(GenomeQuery query) throws CellBaseException {
        List> queryResults = new ArrayList<>();
        for (Region region : query.getRegions()) {
            queryResults.add(genomeDBAdaptor.getSequence(region, query.toQueryOptions(), query.getDataRelease()));
        }

        for (int i = 0; i < query.getRegions().size(); i++) {
            queryResults.get(i).setId(query.getRegions().get(i).toString());
        }
        return queryResults;
    }

    @Deprecated
    public List> getByRegions(QueryOptions queryOptions, String regions, int dataRelease)
            throws CellBaseException {
        List regionList = Region.parseRegions(regions);
        List> queryResults = new ArrayList<>();
        for (Region region : regionList) {
            queryResults.add(genomeDBAdaptor.getSequence(region, queryOptions, dataRelease));
        }

        for (int i = 0; i < regionList.size(); i++) {
            queryResults.get(i).setId(regionList.get(i).toString());
        }
        return queryResults;
    }

    @Deprecated
    public CellBaseDataResult getByRegion(Query query, QueryOptions queryOptions, String regions, String strand,
                                                                 int dataRelease) throws CellBaseException {
        query.put(ParamConstants.QueryParams.REGION.key(), regions);
        query.put("strand", strand);
        CellBaseDataResult queryResult = genomeDBAdaptor.getGenomicSequence(query, queryOptions, dataRelease);
        queryResult.setId(regions);
        return queryResult;
    }

    public List>> getConservation(QueryOptions queryOptions, List regionList,
                                                                               int dataRelease) throws CellBaseException {
        List>> queryResultList = genomeDBAdaptor.getConservation(regionList, queryOptions,
                dataRelease);
        return queryResultList;
    }

    public List>> getConservation(QueryOptions queryOptions, String regions, int dataRelease)
            throws CellBaseException {
        List regionList = Region.parseRegions(regions);
        List>> queryResultList = genomeDBAdaptor.getConservation(regionList, queryOptions,
                dataRelease);
        for (int i = 0; i < regionList.size(); i++) {
            queryResultList.get(i).setId(regions);
        }
        return queryResultList;
    }

    public CellBaseDataResult getConservationScoreRegion(List regions, CellBaseQueryOptions options,
                                                                             int dataRelease) throws CellBaseException {
        Set chunkIdSet = new HashSet<>();
        for (Region region : regions) {
            chunkIdSet.addAll(genomeDBAdaptor.getConservationScoreChunkIds(region));
        }

        return genomeDBAdaptor.getConservationScoreRegion(new ArrayList<>(chunkIdSet), options, dataRelease);
    }

    public List> getAllScoresByRegionList(List regionList, QueryOptions options, int dataRelease)
            throws CellBaseException {
        return genomeDBAdaptor.getAllScoresByRegionList(regionList, options, dataRelease);
    }

    public CellBaseDataResult getSequence(Region region, QueryOptions queryOptions, int dataRelease)
            throws CellBaseException {
        return genomeDBAdaptor.getSequence(region, queryOptions, dataRelease);
    }

    public CellBaseDataResult getGenomicSequence(Query query, QueryOptions queryOptions, int dataRelease)
            throws CellBaseException {
        return genomeDBAdaptor.getGenomicSequence(query, queryOptions, dataRelease);
    }

    public CellBaseDataResult getCytobands(Region region, QueryOptions queryOptions, int dataRelease) throws CellBaseException {
        return genomeDBAdaptor.getCytobands(region, queryOptions, dataRelease);
    }

    public List> getCytobands(List regionList, QueryOptions queryOptions, int dataRelease)
            throws CellBaseException {
        List> cellBaseDataResultList = new ArrayList<>(regionList.size());
        for (Region region : regionList) {
            cellBaseDataResultList.add(getCytobands(region, queryOptions, dataRelease));
        }
        return cellBaseDataResultList;
    }

    public List> getCytobands(List regionList, int dataRelease) throws CellBaseException {
        return getCytobands(regionList, null, dataRelease);
    }

    public CellBaseDataResult getGenomeSequenceRawData(List regions, int dataRelease)
            throws CellBaseException {
        Set chunkIdSet = new HashSet<>();
        for (Region region : regions) {
            chunkIdSet.addAll(genomeDBAdaptor.getGenomeSequenceChunkId(region));
        }
        return genomeDBAdaptor.getGenomeSequenceRawData(new ArrayList<>(chunkIdSet), dataRelease);
    }
}