/**
* Finding next sequence id using key
*
* @param key
* @return
*/
public Long findNextSequenceId(String key) {
// Building query
Query query = new Query();
query.addCriteria(Criteria.where("_id").is(key));
Sequence sequence = findByQuery(query);
return sequence.getSequence();
}
public static Sequence promoteSequence(Sequence x) {
if (BaseSequence.class.isAssignableFrom(x.getClass())) {
try {
return new Sequence(x.getFullName(), x.getSequence());
} catch (SequenceException e) {
return x;
}
} else
// if it's not a BaseSequence, there isn't anything
// to 'promote' to! (yet)
return x;
}
@Override
public Expression visit(Sequence sequence) {
Sequence result = new Sequence();
for (Expression exp : sequence.getSequence()) {
if (exp.getClass() == Choice.class) {
String name = "seq" + Integer.toString(count);
count++;
Nonterminal nt = new Nonterminal(name);
Expression expr = exp.accept(this);
newRules.put(nt, expr);
result.addExpr(nt);
} else {
result.addExpr(exp.accept(this));
}
}
return result;
}
/**
* Updating sequence details
*
* @param key
* @return
*/
public Long updateSequence(String key) {
// Building query
Query query = new Query();
query.addCriteria(Criteria.where("_id").is(key));
// Increase Sequence Id by 1
Update update = new Update();
update.inc("sequence", 1);
FindAndModifyOptions options = new FindAndModifyOptions();
options.returnNew(true);
Sequence sequence = hamesDataStore.findAndModify(query, update, options, Sequence.class);
return sequence.getSequence();
}
protected PartData retrieveEntryDetails(String userId, Entry entry) {
// user must be able to read if not public entry
if (!permissionsController.isPubliclyVisible(entry)) authorization.expectRead(userId, entry);
PartData partData = ModelToInfoFactory.getInfo(entry);
if (partData == null) return null;
boolean hasSequence = sequenceDAO.hasSequence(entry.getId());
partData.setHasSequence(hasSequence);
boolean hasOriginalSequence = sequenceDAO.hasOriginalSequence(entry.getId());
partData.setHasOriginalSequence(hasOriginalSequence);
// permissions
partData.setCanEdit(authorization.canWriteThoroughCheck(userId, entry));
partData.setPublicRead(permissionsController.isPubliclyVisible(entry));
// create audit event if not owner
// todo : remote access check
if (userId != null
&& authorization.getOwner(entry) != null
&& !authorization.getOwner(entry).equalsIgnoreCase(userId)) {
try {
Audit audit = new Audit();
audit.setAction(AuditType.READ.getAbbrev());
audit.setEntry(entry);
audit.setUserId(userId);
audit.setLocalUser(true);
audit.setTime(new Date(System.currentTimeMillis()));
auditDAO.create(audit);
} catch (Exception e) {
Logger.error(e);
}
}
// retrieve more information about linked entries if any (default only contains id)
if (partData.getLinkedParts() != null) {
ArrayList<PartData> newLinks = new ArrayList<>();
for (PartData link : partData.getLinkedParts()) {
Entry linkedEntry = dao.get(link.getId());
if (!authorization.canRead(userId, linkedEntry)) continue;
link = ModelToInfoFactory.createTipView(linkedEntry);
Sequence sequence = sequenceDAO.getByEntry(linkedEntry);
if (sequence != null) {
link.setBasePairCount(sequence.getSequence().length());
link.setFeatureCount(sequence.getSequenceFeatures().size());
}
newLinks.add(link);
}
partData.getLinkedParts().clear();
partData.getLinkedParts().addAll(newLinks);
}
// check if there is a parent available
List<Entry> parents = dao.getParents(entry.getId());
if (parents == null) return partData;
for (Entry parent : parents) {
if (!authorization.canRead(userId, parent)) continue;
if (parent.getVisibility() != Visibility.OK.getValue()
&& !authorization.canWriteThoroughCheck(userId, entry)) continue;
EntryType type = EntryType.nameToType(parent.getRecordType());
PartData parentData = new PartData(type);
parentData.setId(parent.getId());
parentData.setName(parent.getName());
parentData.setVisibility(Visibility.valueToEnum(parent.getVisibility()));
partData.getParents().add(parentData);
}
return partData;
}