/*
 * 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.variation;

import java.sql.Connection;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
//import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.Species;

/**
 * Check that if the peptide_allele_string of transcript_variation is not >1. 
 * It should out >1, unless it filled with numbers
 */
public class VariationSynonym extends SingleDatabaseTestCase {

    /**
     * Creates a new instance of Check Variation Synonym
     */
    public VariationSynonym() {
        addToGroup("variation");
	addToGroup("variation-release");
        setDescription("Check that Venter and Watson should have 3 million variations");
    }

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

        boolean result = true;
	String[] individualNames = {"Venter","Watson"};
	String individualName;
	// Check that Venter and Watson should have 3 million variations

        Connection con = dbre.getConnection();
	if (dbre.getSpecies() == Species.HOMO_SAPIENS){
	    for (int i = 0; i < individualNames.length; i++) {
		individualName = individualNames[i];
		int rows = getRowCount(con, "SELECT COUNT(*) FROM variation v, source s WHERE v.source_id=s.source_id and s.name like '%" + individualName + "'");
		int rows1 = getRowCount(con, "SELECT COUNT(*) FROM variation_synonym vs, source s WHERE vs.source_id=s.source_id and s.name like '%" + individualName + "'");
		int tot_rows = rows + rows1;
		if (tot_rows < 3000000) {
		    result = false;
		    ReportManager.problem(this, con, tot_rows + " with variations for " + individualName);
		} else {
		    //ReportManager.info(this, con, tot_rows + " with variation for " + individualName);
		}
	    }
	}
        if (result){
        	ReportManager.correct(this,con,"Venter/Watson has more then 3 million variations");
        }
        return result;

    } // run

} // VariationSynonym

/*
 * 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.variation;

import java.sql.Connection;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
//import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.Species;

/**
 * Check that if the peptide_allele_string of transcript_variation is not >1. 
 * It should out >1, unless it filled with numbers
 */
public class VariationSynonym extends SingleDatabaseTestCase {

    /**
     * Creates a new instance of Check Variation Synonym
     */
    public VariationSynonym() {
        addToGroup("variation");
	addToGroup("variation-release");
        setDescription("Check that Venter and Watson should have 3 million variations");
    }

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

        boolean result = true;
	String[] individualNames = {"Venter","Watson"};
	String individualName;
	// Check that Venter and Watson should have 3 million variations

        Connection con = dbre.getConnection();
	if (dbre.getSpecies() == Species.HOMO_SAPIENS){
	    for (int i = 0; i < individualNames.length; i++) {
		individualName = individualNames[i];
		int rows = getRowCount(con, "SELECT COUNT(*) FROM variation v, source s WHERE v.source_id=s.source_id and s.name like '%" + individualName + "'");
		int rows1 = getRowCount(con, "SELECT COUNT(*) FROM variation_synonym vs, source s WHERE vs.source_id=s.source_id and s.name like '%" + individualName + "'");
		int tot_rows = rows + rows1;
		if (tot_rows < 3000000) {
		    result = false;
		    ReportManager.problem(this, con, tot_rows + " with variations for " + individualName);
		} else {
		    ReportManager.correct(this,con,"Venter/Watson has more then 3 million variations");
		}
	    }
	}
	if (result){
	    ReportManager.info(this,con,"This test is only for human at moment");
	}
	
	return result;
	
    } // run

} // VariationSynonym

make small change to report info for non-human species