/*
 * The Exomiser - A tool to annotate and prioritize genomic variants
 *
 * Copyright (c) 2016-2019 Queen Mary University of London.
 * Copyright (c) 2012-2016 Charité Universitätsmedizin Berlin and Genome Research Ltd.
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.monarchinitiative.exomiser.core.genome.dao;

import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.monarchinitiative.exomiser.core.model.StructuralType;
import org.monarchinitiative.exomiser.core.model.Variant;
import org.monarchinitiative.exomiser.core.model.VariantAnnotation;
import org.monarchinitiative.exomiser.core.model.pathogenicity.PathogenicityData;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit.jupiter.SpringExtension;

/**
 * @author Jules Jacobsen <j.jacobsen@qmul.ac.uk>
 */
@ExtendWith(SpringExtension.class)
@ContextConfiguration(classes = {TestSvDataSourceConfig.class, SvPathogenicityDao.class})
class SvPathogenicityDaoTest {

    @Autowired
    private SvPathogenicityDao instance;

    @Test
    void getDupExactMatch() {
        Variant variant = VariantAnnotation.builder()
                .chromosome(17)
                .start(526)
                .end(81_041_938)
                .structuralType(StructuralType.DUP)
                .build();

        PathogenicityData result = instance.getPathogenicityData(variant);

        System.out.println(result);
    }

    @Test
    void getDupInexactMatch() {
        Variant variant = VariantAnnotation.builder()
                .chromosome(17)
                .start(500)
                .end(82_041_938)
                .structuralType(StructuralType.DUP)
                .build();

        PathogenicityData result = instance.getPathogenicityData(variant);

        System.out.println(result);
    }

    @Test
    void getInsExactMatch() {
        Variant variant = VariantAnnotation.builder()
                .chromosome(10)
                .start(105_817_214)
                .end(105_817_214)
                .structuralType(StructuralType.DUP)
                .build();

        PathogenicityData result = instance.getPathogenicityData(variant);

        System.out.println(result);
    }
}
@@ -947,16 +947,55 @@
 e.dao;%0A%0A
+import org.junit.jupiter.api.Disabled;%0A
 import o
@@ -1600,16 +1600,26 @@
 uk%3E%0A */%0A
+@Disabled%0A
 @ExtendW

Disable SvPathogenicityDaoTest until test data is in place