org.opencb.cellbase.lib.download.CaddDownloadManager 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.download;

import org.opencb.cellbase.core.config.CellBaseConfiguration;
import org.opencb.cellbase.core.exception.CellBaseException;
import org.opencb.cellbase.lib.EtlCommons;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Collections;
import java.util.List;

public class CaddDownloadManager extends AbstractDownloadManager {

    private static final String CADD_NAME = "CADD";
    public CaddDownloadManager(String species, String assembly, Path targetDirectory, CellBaseConfiguration configuration)
            throws IOException, CellBaseException {
        super(species, assembly, targetDirectory, configuration);
    }

    @Override
    public List download() throws IOException, InterruptedException {
        return Collections.singletonList(downloadCaddScores());
    }

    public DownloadFile downloadCaddScores() throws IOException, InterruptedException {
        if (!speciesHasInfoToDownload(speciesConfiguration, "variation_functional_score")) {
            return null;
        }
        if (speciesConfiguration.getScientificName().equals("Homo sapiens")) {
            logger.info("Downloading CADD scores information ...");

            Path variationFunctionalScoreFolder = downloadFolder.resolve("variation_functional_score");
            Files.createDirectories(variationFunctionalScoreFolder);

            // Downloads CADD scores
            String url = configuration.getDownload().getCadd().getHost();

            saveVersionData(EtlCommons.VARIATION_FUNCTIONAL_SCORE_DATA, CADD_NAME, url.split("/")[5], getTimeStamp(),
                    Collections.singletonList(url), variationFunctionalScoreFolder.resolve("caddVersion.json"));
            return downloadFile(url, variationFunctionalScoreFolder.resolve("whole_genome_SNVs.tsv.gz").toString());
        }
        return null;
    }
}