VariantImporter.java

package org.opencb.opencga.storage.core.variant.io;

import org.opencb.opencga.storage.core.exceptions.StorageEngineException;
import org.opencb.opencga.storage.core.metadata.ExportMetadata;
import org.opencb.opencga.storage.core.metadata.StudyConfiguration;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;

import java.io.IOException;
import java.net.URI;
import java.util.Map;
import java.util.function.Function;
import java.util.stream.Collectors;

/**
 * Created on 07/12/16.
 *
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public abstract class VariantImporter {

    protected final VariantDBAdaptor dbAdaptor;

    public VariantImporter(VariantDBAdaptor dbAdaptor) {
        this.dbAdaptor = dbAdaptor;
    }

    public void importData(URI inputUri) throws StorageEngineException, IOException {
        VariantMetadataImporter metadataImporter = new VariantMetadataImporter();
        ExportMetadata exportMetadata = metadataImporter.importMetaData(inputUri, dbAdaptor.getStudyConfigurationManager());

        importData(inputUri, exportMetadata);
    }

    public void importData(URI input, ExportMetadata remappedMetadata) throws StorageEngineException, IOException {
        Map<StudyConfiguration, StudyConfiguration> map = remappedMetadata.getStudies().stream()
                .collect(Collectors.toMap(Function.identity(), Function.identity()));
        importData(input, remappedMetadata, map);
    }

    public abstract void importData(URI input, ExportMetadata remappedMetadata,
                                    Map<StudyConfiguration, StudyConfiguration> studiesOldNewMap)
            throws StorageEngineException, IOException;

}