/*
 * Copyright (C) 2003 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.generic;

import org.ensembl.healthcheck.DatabaseRegistry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.testcase.MultiDatabaseTestCase;

/**
 * Check meta table species, classification and taxonomy_id is the same in all DBs for each species
 */

public class MetaCrossSpecies extends MultiDatabaseTestCase {

    private DatabaseType[] types = {DatabaseType.CORE, DatabaseType.EST, DatabaseType.ESTGENE, DatabaseType.VEGA};

    /**
     * Create a new instance of MetaCrossSpecies
     */
    public MetaCrossSpecies() {
        addToGroup("post_genebuild");
        addToGroup("release");
        setDescription("Check meta table species, classification and taxonomy_id is the same in all DBs for each species");
    }

    /**
     * Check various aspects of the meta table.
     * 
     * @param dbr
     *          The database registry containing all the specified databases.
     * @return True if the meta information is consistent within species.
     */
    public boolean run(DatabaseRegistry dbr) {

        boolean result = checkSQLAcrossSpecies(
                "SELECT LCASE(meta_value) FROM meta WHERE meta_key LIKE \'species.%' ORDER BY meta_value", dbr, types);
        if (!result) {
            ReportManager.problem(this, "", "meta information not the same for some databases");
        } else {
            ReportManager.correct(this, "", "meta information is the same for all databases for all species");
        }

        return result;

    }

} // MetaCrossSpecies

@@ -1260,19 +1260,20 @@
 aseType.
-EST
+CDNA
 , Databa
@@ -1283,15 +1283,21 @@
 ype.
-ESTGENE
+OTHERFEATURES
 , Da

Update database types (otherfeatures instead of EST)