/*
 * 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 java.sql.Connection;
import java.util.HashMap;
import java.util.Map;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.util.Utils;

/**
 * Compare the counts of the number of rows in each table in this and the previous database.
 */

public class ComparePreviousVersionTableRows extends ComparePreviousVersionBase {

	/**
	 * Create a new XrefTypes testcase.
	 */
	public ComparePreviousVersionTableRows() {

		addToGroup("post_genebuild");
		addToGroup("release");
		setDescription("Compare the counts of the number of rows in each table in this and the previous database");

	}

	// ----------------------------------------------------------------------

	protected Map getCounts(DatabaseRegistryEntry dbre) {

		Map rowCounts = new HashMap();
		
		Connection con = dbre.getConnection();
		
		String[] tables = getTableNames(con);
		tables = Utils.removeStringFromArray(tables, "meta");
		//we need a different query for xref, and only compare those that are not projected
		tables = Utils.removeStringFromArray(tables, "external_synonym");
		
		for (int i = 0; i < tables.length; i++) {
			
			rowCounts.put(tables[i], new Integer(getRowCount(con, "SELECT COUNT(*) FROM " + tables[i])));
			
		}
		rowCounts.put("external_synonym",new Integer(getRowCount(con,"SELECT COUNT(*) FROM external_synonym e, xref x WHERE e.xref_id = x.xref_id AND x.info_type <> 'PROJECTION'")));
		
		return rowCounts;

	}

	// ------------------------------------------------------------------------

	protected String entityDescription() {

		return "rows in";

	}

	// ------------------------------------------------------------------------

	protected double threshold() {

		return 0.75;

	}

	// ------------------------------------------------------------------------

} // ComparePreviousVersionBiotypes

@@ -2637,13 +2637,14 @@
 sion
-Biotype
+TableRow
 s%0A

Comment fix