/**
* Get all observation targets that are not in a given batch.
*
* @param batchId : the id of the batch to test for
* @return
* @throws DatabaseException
* @throws ParseException
*/
public List<ObservationTarget> getObservationTargetsNotInCurrentBatch(Database db, int batchId)
throws DatabaseException, ParseException {
List<ObservationTarget> result = new ArrayList<ObservationTarget>();
List<ObservationTarget> targets = db.query(ObservationTarget.class).sortASC("name").find();
for (ObservationTarget target : targets) {
Query<MolgenisBatchEntity> q = db.query(MolgenisBatchEntity.class);
q.addRules(new QueryRule(MolgenisBatchEntity.BATCH, Operator.EQUALS, batchId));
q.addRules(new QueryRule(MolgenisBatchEntity.OBJECTID, Operator.EQUALS, target.getId()));
List<MolgenisBatchEntity> l = q.find();
if (l.size() == 0) {
result.add(target);
}
}
return result;
}
/**
* Get all observation targets that are not in any batch.
*
* @return
* @throws DatabaseException
* @throws ParseException
*/
public List<ObservationTarget> getObservationTargetsNotInBatch(Database db)
throws DatabaseException, ParseException {
List<ObservationTarget> result = new ArrayList<ObservationTarget>();
List<ObservationTarget> targets = db.query(ObservationTarget.class).sortASC("name").find();
for (ObservationTarget target : targets) {
List<MolgenisBatchEntity> l =
db.query(MolgenisBatchEntity.class)
.equals(MolgenisBatchEntity.OBJECTID, target.getId())
.find();
if (l.size() == 0) {
result.add(target);
}
}
return result;
}
public void addToBatch(Database db, Integer batchId, List<Integer> targetIds)
throws DatabaseException, ParseException, IOException {
for (Integer targetId : targetIds) {
ObservationTarget target = db.findById(ObservationTarget.class, targetId);
// TODO: Danny use or loose
/*List<OntologyTerm> terms = db.query(OntologyTerm.class).equals(OntologyTerm.NAME, target.getClass().toString()).find();*/
// if (terms.size() != 1)
// throw new DatabaseException("No OntologyTerm found for " +
// target.getClass().toString());
MolgenisBatchEntity entity = new MolgenisBatchEntity();
// entity.setEntityType(terms.get(0));
entity.setBatch(batchId);
entity.setName(target.getName());
entity.setObjectId(target.getId());
db.add(entity);
}
}