/*
* Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
* Copyright [2016-2017] 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.compara;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.List;
import java.util.Vector;
import org.ensembl.healthcheck.DatabaseRegistry;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Species;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.compara.AbstractComparaTestCase;
import org.ensembl.healthcheck.util.DBUtils;
import org.ensembl.healthcheck.util.DefaultMapRowMapper;
/**
* Check that the main species-set names are similar to the previous
* database
*/
public class CompareMSANames extends AbstractComparaTestCase {
/**
* Create an ForeignKeyMethodLinkSpeciesSetId that applies to a specific set
* of databases.
*/
public CompareMSANames() {
setDescription("Check the content of the species_set_tag table");
setTeamResponsible(Team.COMPARA);
}
/**
* Run the test.
*
* @param comparaDbre
* The database to use.
* @return true if the test passed.
*
*/
public boolean run(DatabaseRegistryEntry comparaDbre) {
boolean result = true;
DatabaseRegistryEntry[] allSecondaryComparaDBs = DBUtils.getSecondaryDatabaseRegistry("compara").getAll(DatabaseType.COMPARA);
if (allSecondaryComparaDBs.length == 0) {
result = false;
ReportManager.problem(this,
comparaDbre.getConnection(),
"Cannot find the compara database in the secondary server. This check expects to find a previous version of the compara database for checking that all the *named* species_sets are still present in the current database.");
}
for (DatabaseRegistryEntry secondaryComparaDbre: allSecondaryComparaDBs) {
// Check vs previous compara DB.
result &= checkSetOfSpeciesSets(comparaDbre, secondaryComparaDbre);
}
return result;
}
public boolean checkSetOfSpeciesSets(DatabaseRegistryEntry primaryComparaDbre, DatabaseRegistryEntry secondaryComparaDbre) {
boolean result = true;
Connection con1 = primaryComparaDbre.getConnection();
Connection con2 = secondaryComparaDbre.getConnection();
// Get list of species_set sets in the secondary server
String sql = "SELECT species_set_header.name, COUNT(*) "
+ " FROM method_link_species_set JOIN method_link USING (method_link_id) JOIN species_set_header USING (species_set_id) "
+ " WHERE (class LIKE '%multiple_alignment%' OR class LIKE '%tree_alignment%' OR class LIKE '%ancestral_alignment%') AND species_set_header.name != ''"
+ " GROUP BY species_set_header.name";
Map<String,Integer> primarySets = DBUtils.getSqlTemplate(con1).queryForMap(sql, new DefaultMapRowMapper<String, Integer>(String.class, Integer.class));
Map<String,Integer> secondarySets = DBUtils.getSqlTemplate(con2).queryForMap(sql, new DefaultMapRowMapper<String, Integer>(String.class, Integer.class));
for (Map.Entry<String, Integer> key_value : secondarySets.entrySet()) {
String key = key_value.getKey();
Integer primaryValue = primarySets.get(key);
Integer secondaryValue = key_value.getValue();
if (!primarySets.containsKey(key)) {
ReportManager.problem(this, con1, String.format("Species set '%s' is missing (it appears %d time(s) in %s", key, secondaryValue, DBUtils.getShortDatabaseName(con2)));
result = false;
} else if (primaryValue < secondaryValue) {
ReportManager.problem(this, con1, String.format("Species set '%s' is present only %d times instead of %d as in %s", key, primaryValue, secondaryValue, DBUtils.getShortDatabaseName(con2)));
result = false;
}
}
for (Map.Entry<String, Integer> key_value : primarySets.entrySet()) {
String next = key_value.getKey();
if (!secondarySets.containsKey(next)) {
ReportManager.problem(this, con1, String.format("Species set '%s' is new (compared to %s)", next, DBUtils.getShortDatabaseName(con2)));
result = false;
}
}
return result;
}
} // CompareMSANames