private boolean checkCodingCountAttributes(final DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String code = (dbre.getType() == DatabaseType.SANGER_VEGA) ? "KnwnPCCount" : "coding_cnt";
SqlTemplate t = DBUtils.getSqlTemplate(dbre);
String sql =
"select distinct g.seq_region_id from gene g where g.biotype = ? and g.seq_region_id not in (select distinct g.seq_region_id from gene g, seq_region_attrib sa, attrib_type at where g.seq_region_id = sa.seq_region_id and sa.attrib_type_id = at.attrib_type_id and at.code in (?,?))";
List<String> toplevel =
t.queryForDefaultObjectList(sql, String.class, "protein_coding", "LRG", "non_ref");
sql =
"select distinct g.seq_region_id from gene g, seq_region_attrib sa, attrib_type at where g.seq_region_id = sa.seq_region_id and sa.attrib_type_id = at.attrib_type_id and code =? ";
List<String> known = t.queryForDefaultObjectList(sql, String.class, code);
Set<String> missing = new HashSet<String>(toplevel);
missing.removeAll(known);
if (missing.isEmpty()) {
ReportManager.correct(
this,
con,
"All seq_regions with protein_coding genes have a coding_cnt attribute associated with them");
} else {
String msg =
String.format(
"%s regions with protein_coding genes do not have the coding_cnt attribute associated",
missing.size());
ReportManager.problem(this, con, msg);
result = false;
}
return result;
}
protected int fetchToplevelSeqRegionCount() {
List<Integer> numSeqRegionsList =
sqlTemplateTestDb.queryForDefaultObjectList(
"select count(*) from seq_region join seq_region_attrib using (seq_region_id) join attrib_type using (attrib_type_id) where code='toplevel'",
Integer.class);
assertLengthIsOne(numSeqRegionsList);
Integer numSeqRegions = numSeqRegionsList.get(0);
return numSeqRegions;
}
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
init(dbre);
List<Integer> allSpeciesIds =
sqlTemplateTestDb.queryForDefaultObjectList(
"select distinct species_id from meta where species_id is not null", Integer.class);
if (allSpeciesIds.size() == 0) {
ReportManager.problem(this, testDbConn, "No species configured!");
}
boolean allSpeciesPassed = true;
for (int speciesId : allSpeciesIds) {
allSpeciesPassed &= runTestForSpecies(dbre, speciesId);
}
return allSpeciesPassed;
}
/**
* @param sqlTemplateTestDb
* @param metaKey
* @return
*/
protected String fetchSingleMetaValueFor(
final SqlTemplate sqlTemplateTestDb, int speciesId, String metaKey) {
String sql =
"select meta_value from meta where meta.meta_key = '"
+ metaKey
+ "' and species_id="
+ speciesId;
List<String> metaValueList = sqlTemplateTestDb.queryForDefaultObjectList(sql, String.class);
if (metaValueList.size() > 1) {
throw new RuntimeException(
"Got more than one meta_value for metaKey " + metaKey + ". Expected only one!\n" + sql);
}
if (metaValueList.size() == 0) {
throw new RuntimeException("Metakey " + metaKey + " is missing in the meta table!\n" + sql);
}
String metaValue = metaValueList.get(0);
return metaValue;
}