public QueryResult<VariantAnalysisInfo> getAnalysisInfo(String studyId) {
long start = System.currentTimeMillis();
QueryResult<VariantAnalysisInfo> qres = new QueryResult<>();
VariantAnalysisInfo vi = new VariantAnalysisInfo();
DBCollection coll = db.getCollection("sources");
DBCollection collV = db.getCollection("variants");
long dbStart = System.currentTimeMillis();
DBObject study = coll.findOne(new BasicDBObject("alias", studyId));
if (study != null) {
Iterator<Object> it = ((BasicDBList) study.get("samples")).iterator();
while (it.hasNext()) {
vi.addSample((String) it.next());
}
BasicDBObject gs = (BasicDBObject) study.get("globalStats");
for (String elem : gs.keySet()) {
if (!elem.equalsIgnoreCase("consequenceTypes")) {
double val = gs.getDouble(elem);
vi.addGlobalStats(elem, val);
} else {
BasicDBObject cts = (BasicDBObject) gs.get("consequenceTypes");
for (String ct : cts.keySet()) {
vi.addConsequenceType(ct, cts.getInt(ct));
}
}
}
}
qres.setDbTime(System.currentTimeMillis() - dbStart);
qres.setResult(Arrays.asList(vi));
qres.setTime(System.currentTimeMillis() - start);
return qres;
}
@Test(groups = "dev")
public void collectionTest() {
DB db = mongo.getDB(DBNAME);
DBCollection myCollection = db.getCollection("myCollection");
myCollection.save(
new BasicDBObject(
MapUtils.putAll(new HashMap(), new Object[] {"name", "leon", "age", 33})));
myCollection.findOne();
Set<String> names = db.getCollectionNames();
assertNotNull(names);
boolean hit = false;
for (String name : names) {
if ("myCollection".equals(name)) {
hit = true;
break;
}
}
assertTrue(hit);
}
