/**
* Check that any _rna_edit attribute represents a substitution rather than an insertion or
* deletion
*/
private boolean checkRnaEditAttributes(final DatabaseRegistryEntry dbre) {
boolean ok = true;
RowMapper<Attrib> mapper =
new RowMapper<Attrib>() {
public Attrib mapRow(ResultSet rs, int row) throws SQLException {
return new Attrib(rs.getString(1), rs.getLong(2), rs.getString(3));
}
};
String sql =
"select sr.name, sr.seq_region_id, sra.value "
+ "from seq_region sr join seq_region_attrib sra using (seq_region_id) "
+ "join attrib_type at using (attrib_type_id) where at.code =?";
List<Attrib> attributes = getSqlTemplate(dbre).queryForList(sql, mapper, "_rna_edit");
for (Attrib a : attributes) {
if (!a.isOk()) {
ReportManager.warning(this, dbre.getConnection(), a.toString());
ok = false;
}
}
if (!ok) {
ReportManager.problem(
this,
dbre.getConnection(),
"Detected sequence regions with incorrectly formatted _rna_edit attributes. Check warnings");
}
return ok;
}
/** Check that the schema_version in the meta table is present and matches the database name. */
private boolean checkSchemaVersionDBName(DatabaseRegistryEntry dbre) {
boolean result = true;
// get version from database name
String dbNameVersion = dbre.getSchemaVersion();
logger.finest("Schema version from database name: " + dbNameVersion);
// get version from meta table
Connection con = dbre.getConnection();
if (dbNameVersion == null) {
ReportManager.warning(this, con, "Can't deduce schema version from database name.");
return false;
}
String schemaVersion =
DBUtils.getRowColumnValue(
con, "SELECT meta_value FROM meta WHERE meta_key='schema_version'");
logger.finest("schema_version from meta table: " + schemaVersion);
if (schemaVersion == null || schemaVersion.length() == 0) {
ReportManager.problem(this, con, "No schema_version entry in meta table");
return false;
} else if (!schemaVersion.matches("[0-9]+")) {
ReportManager.problem(this, con, "Meta schema_version " + schemaVersion + " is not numeric");
return false;
} else if (!dbNameVersion.equals(schemaVersion) && !isSangerVega) { // do
// not
// report
// for
// sangervega
ReportManager.problem(
this,
con,
"Meta schema_version "
+ schemaVersion
+ " does not match version inferred from database name ("
+ dbNameVersion
+ ")");
return false;
} else {
ReportManager.correct(
this,
con,
"schema_version " + schemaVersion + " matches database name version " + dbNameVersion);
}
return result;
}