/*
 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 ForeignKeyMethodLinkId extends SingleDatabaseTestCase {

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

        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, "method_link")) {

            result &= checkForOrphans(con, "method_link_species_set", "method_link_id", "method_link", "method_link_id");
            result &= checkForOrphans(con, "method_link", "method_link_id", "method_link_species_set", "method_link_id");

        } else {
            ReportManager.correct(this, con, "NO ENTRIES in method_link table, so nothing to test IGNORED");
        }

        return result;

    }

} // ForeignKeyMethodLinkId

@@ -1744,16 +1744,17 @@
     if (
+!
 tableHas
@@ -1777,25 +1777,24 @@
 d_link%22)) %7B%0A
-%0A
             
@@ -1797,117 +1797,312 @@
     
-result &= checkForOrphans(con, %22method_link_species_set%22, %22method_link_id%22, %22method_link%22, %22method_link_id%22);
+ReportManager.correct(this, con, %22NO ENTRIES in method_link table, so nothing to test IGNORED%22);%0A%0A        %7D else if (!tableHasRows(con, %22method_link_species_set%22)) %7B%0A            ReportManager.correct(this, con, %22NO ENTRIES in method_link_species_set table, so nothing to test IGNORED%22);%0A%0A        %7D else %7B
 %0A   
@@ -2153,16 +2153,28 @@
 hod_link
+_species_set
 %22, %22meth
@@ -2194,36 +2194,24 @@
 %22method_link
-_species_set
 %22, %22method_l
@@ -2216,33 +2216,32 @@
 _link_id%22);%0A
-%0A
         
 %7D else %7B%0A   
@@ -2232,122 +2232,118 @@
     
-%7D else %7B%0A            ReportManager.correct(this, con, %22NO ENTRIES in method_link table, so nothing to test IGNORED
+    result &= checkForOrphans(con, %22method_link%22, %22method_link_id%22, %22method_link_species_set%22, %22method_link_id
 %22);%0A

Check method_link_species_set table has rows