/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2018] EMBL-European Bioinformatics Institute
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *      http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.ensembl.healthcheck.testcase.variation;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.Species;

/**
 * An EnsEMBL Healthcheck test case that looks for variation feature entries
 * with no alleles
 */

public class VariationFeatureAlleles extends SingleDatabaseTestCase {

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

        setDescription("Check for variation features with no alleles.");
        setTeamResponsible(Team.VARIATION);

    }

    /**
     * Look for variation feature entries with no alleles
     * 
     * @param dbre
     *            The database to use.
     * @return true Ff all foreign key relationships are valid.
     */
    public boolean run(DatabaseRegistryEntry dbre) {

        // Alleles are no longer stored for human variants without frequency data
        Species species = dbre.getSpecies();
        if (species == Species.HOMO_SAPIENS ){
          return true;
        }

        return checkForOrphans(dbre.getConnection(), "variation_feature", "variation_id", "allele", "variation_id",
                true);
    }

} 

@@ -784,16 +784,45 @@
 ation;%0A%0A
+import java.sql.Connection;%0A%0A
 import o
@@ -1007,16 +1007,107 @@
 Species;
+%0Aimport org.ensembl.healthcheck.ReportManager;%0Aimport org.ensembl.healthcheck.util.DBUtils;
 %0A%0A/**%0A *
@@ -1788,24 +1788,782 @@
 ry dbre) %7B%0A%0A
+      Connection con = dbre.getConnection();%0A      boolean result = true;%0A%0A      try %7B%0A        // Look for missing alleles in allele strings%0A        String stmt = %22SELECT COUNT(variation_feature_id) FROM variation_feature WHERE allele_string LIKE '%25/' OR allele_string like '%25//%25' %22;%0A        int rows = DBUtils.getRowCount(con,stmt);%0A        if (rows %3E 0) %7B%0A          result = false;%0A          ReportManager.problem(this, con, String.valueOf(rows) + %22 rows have missing alleles in allele_string in variation_feature%22);%0A          ReportManager.problem(this, con, %22USEFUL SQL: %22 + stmt);%0A        %7D%0A      %7D catch (Exception e) %7B%0A         ReportManager.problem(this, con, %22HealthCheck caused an exception: %22 + e.getMessage());%0A         result = false;%0A       %7D%0A%0A
         // A
@@ -2745,16 +2745,25 @@
 urn true
+ & result
 ;%0A      
@@ -2777,20 +2777,23 @@
       re
-turn
+sult &=
  checkFo
@@ -2889,30 +2889,37 @@
 id%22,
-%0A                true)
+ true);%0A        return result
 ;%0A  

add HC for allele string