/**
* Test various things about marker features.
*
* @param dbre The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// only check for human, mouse, rat and zebrafish
Species s = dbre.getSpecies();
if ((dbre.getType() != DatabaseType.SANGER_VEGA
&& (s.equals(Species.HOMO_SAPIENS)
|| s.equals(Species.MUS_MUSCULUS)
|| s.equals(Species.RATTUS_NORVEGICUS)))
|| s.equals(Species.DANIO_RERIO)) { // for
// sangervega
// only
// run
// the
// test
// for
// zebrafish
result &= checkFeaturesAndMapWeights(con);
result &= checkMarkerPriorities(con);
result &= checkAllChromosomesHaveMarkers(con);
}
return result;
} // run
/**
* Re-implementation of the compare tables in schema method used to detect if two schemas are
* equal to each other. This is due to variation specific logic which means that schemas can
* differ but this is still valid.
*
* <p>The logic is the same as variation's original version
*
* @param master The master connection
* @param targetDbre The registry entry for the given target schema
* @param ignoreBackupTables Ignored option
* @param directionFlag Ignored option
*/
@Override
public boolean compareTableEquality(
Connection master,
DatabaseRegistryEntry targetDbre,
boolean ignoreBackupTables,
int directionFlag) {
boolean result = true;
Connection target = targetDbre.getConnection();
String targetName = getDbNameForMsg(target);
String masterName = getDbNameForMsg(master);
Set<String> targetTables = createLinkedHashSet(getTableNames(target));
Set<String> masterTables = createLinkedHashSet(getTableNames(master));
Species species = targetDbre.getSpecies();
Set<String> notRequired = getSets(notRequiredTables(), species);
Set<String> required = getSets(requiredTables(), species);
// Check that tables that are in the master are in the target & skip those
// in the notRequired list
for (String masterTable : masterTables) {
if (notRequired.contains(masterTable)) {
String msg =
String.format(
"Table `%s` is in the list of 'notRequiredTables()' exceptions for %s. Skipping",
masterTable, species.getAlias());
ReportManager.info(this, target, msg);
continue;
}
if (!targetTables.contains(masterTable)) {
String msg =
String.format(
"Table `%s` exists in `%s` but not in `%s`", masterTable, masterName, targetName);
ReportManager.problem(this, target, msg);
result = false;
}
}
// Check that tables in the target are in the master & it was a required table
for (String targetTable : targetTables) {
if (!masterTables.contains(targetTable) && !required.contains(targetTable)) {
String msg =
String.format(
"Table `%s` exists in `%s` but not in `%s`", targetTable, targetName, masterName);
ReportManager.problem(this, target, msg);
result = false;
}
}
// Finally check for the required tables
for (String table : required) {
if (!targetTables.contains(table)) {
String msg = String.format("Table `%s` does not exist in `%s`", table, targetName);
ReportManager.problem(this, target, msg);
result = false;
}
}
return result;
}