/*
 Copyright (C) 2004 EBI, GRL
 
 This library is free software; you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public
 License as published by the Free Software Foundation; either
 version 2.1 of the License, or (at your option) any later version.
 
 This library 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
 Lesser General Public License for more details.
 
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 */

package org.ensembl.healthcheck.testcase.compara;

import java.sql.Connection;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;

/**
 * An EnsEMBL Healthcheck test case that looks for broken foreign-key
 * relationships.
 */

public class ForeignKeyGenomicAlignId extends SingleDatabaseTestCase {

    /**
     * Create an ForeignKeyGenomicAlignBlockId that applies to a specific set of databases.
     */
    public ForeignKeyGenomicAlignId() {

        addToGroup("compara_db_constraints");
        setDescription("Check for broken foreign-key relationships in ensembl_compara databases.");

    }

    /**
     * Run the test.
     * 
     * @param dbre
     *          The database to use.
     * @return true if the test passed.
     *  
     */
    public boolean run(DatabaseRegistryEntry dbre) {

        boolean result = true;

       Connection con = dbre.getConnection();

        if (tableHasRows(con, "genomic_align_group") &&
            tableHasRows(con, "genomic_align")) {

            //            result &= checkForOrphans(con, "genomic_align", "genomic_align_id", "genomic_align_group", "genomic_align_id");
            result &= checkForOrphans(con, "genomic_align_group", "genomic_align_id", "genomic_align", "genomic_align_id");
 
        } else {
            ReportManager.correct(this, con, "NO ENTRIES in genomic_align_group or in genomic_align tables, so nothing to test IGNORED");
        }

        return result;

    }

} // ForeignKeyGenomicAlignId

@@ -2112,16 +2112,852 @@
 gn_id%22);
+%0A%0A            // Check that all method_link_species_set_ids match the genomic_align_block table%0A            int mismatches = getRowCount(con, %22SELECT COUNT(*) FROM genomic_align ga LEFT JOIN genomic_align_block gab%22 +%0A                %22 USING (genomic_align_block_id) WHERE ga.method_link_species_set_id != gab.method_link_species_set_id%22);%0A            if (mismatches %3E 0) %7B%0A                ReportManager.problem(this, con, mismatches + %22 entries in genomic_align table have a wrong%22 +%0A                    %22 method_link_species_set_id according to genomic_align_block table%22);%0A                result = false;%0A            %7D else %7B%0A                ReportManager.correct(this, con, %22All entries in genomic_align table have a correct%22 +%0A                    %22 method_link_species_set_id according to genomic_align_block table%22);%0A            %7D
 %0A %0A     

Check that all method_link_species_set_ids match the genomic_align_block table