/** 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;
}
/** Check that all chromomes have > 0 markers_map_locations and marker_features. */
private boolean checkAllChromosomesHaveMarkers(Connection con) {
boolean result = true;
// find all the chromosomes, and for each one check that it has some
// markers
// note a "chromosome" is assumed to be a seq_region that is:
// - on the top-level co-ordinate system and
// - doesn't have and _ or . in the name and
// - has a seq_region name of less than 3 characters
// - doesn't have a name starting with "Un" or "MT"
// get top level co-ordinate system ID
String sql = "SELECT coord_system_id FROM coord_system WHERE rank=1 LIMIT 1";
String s = DBUtils.getRowColumnValue(con, sql);
if (s.length() == 0) {
System.err.println(
"Error: can't get top-level co-ordinate system for " + DBUtils.getShortDatabaseName(con));
return false;
}
int topLevelCSID = Integer.parseInt(s);
try {
// check each top-level seq_region (up to a limit) to see how many
// marker_map_locations and marker features there are
Statement stmt = con.createStatement();
ResultSet rs =
stmt.executeQuery(
"SELECT * FROM seq_region WHERE coord_system_id="
+ topLevelCSID
+ " AND name NOT LIKE '%\\_%' AND name NOT LIKE '%.%' AND name NOT LIKE 'Un%' AND name NOT LIKE 'MT%' AND LENGTH(name) < 3 ORDER BY name");
int numTopLevel = 0;
while (rs.next() && numTopLevel++ < MAX_TOP_LEVEL) {
long seqRegionID = rs.getLong("seq_region_id");
String seqRegionName = rs.getString("name");
// check marker_map_locations
logger.fine("Counting marker_map_locations on chromosome " + seqRegionName);
sql =
"SELECT COUNT(*) FROM marker_map_location WHERE chromosome_name='"
+ seqRegionName
+ "'";
int rows = DBUtils.getRowCount(con, sql);
if (rows == 0) {
ReportManager.problem(
this,
con,
"Chromosome "
+ seqRegionName
+ " (seq_region_id "
+ seqRegionID
+ ") has no entries in marker_map_location");
result = false;
} else {
ReportManager.correct(
this, con, "Chromosome " + seqRegionName + " has " + rows + " marker_map_locations");
}
// check marker_features
logger.fine("Counting marker_features on chromosome " + seqRegionName);
sql = "SELECT COUNT(*) FROM marker_feature WHERE seq_region_id=" + seqRegionID;
rows = DBUtils.getRowCount(con, sql);
if (rows == 0) {
ReportManager.problem(
this,
con,
"Chromosome "
+ seqRegionName
+ " (seq_region_id "
+ seqRegionID
+ ") has no marker_features");
result = false;
} else {
ReportManager.correct(
this, con, "Chromosome " + seqRegionName + " has " + rows + " marker_features");
}
}
rs.close();
stmt.close();
if (numTopLevel == MAX_TOP_LEVEL) {
logger.warning("Only checked first " + numTopLevel + " seq_regions");
}
} catch (SQLException se) {
se.printStackTrace();
}
return result;
}