public ArrayList<TraceSequenceAnalysis> getTraceSequences(String userId, long entryId) {
Entry entry = dao.get(entryId);
if (entry == null) return null;
authorization.expectRead(userId, entry);
List<TraceSequence> sequences = DAOFactory.getTraceSequenceDAO().getByEntry(entry);
ArrayList<TraceSequenceAnalysis> analysisArrayList = new ArrayList<>();
if (sequences == null) return analysisArrayList;
AccountController accountController = new AccountController();
for (TraceSequence traceSequence : sequences) {
TraceSequenceAnalysis analysis = traceSequence.toDataTransferObject();
AccountTransfer accountTransfer = new AccountTransfer();
String depositor = traceSequence.getDepositor();
boolean canEdit = canEdit(userId, depositor, entry);
analysis.setCanEdit(canEdit);
Account account = accountController.getByEmail(traceSequence.getDepositor());
if (account != null) {
accountTransfer.setFirstName(account.getFirstName());
accountTransfer.setLastName(account.getLastName());
accountTransfer.setEmail(account.getEmail());
accountTransfer.setId(account.getId());
}
analysis.setDepositor(accountTransfer);
analysisArrayList.add(analysis);
}
return analysisArrayList;
}
public UserComment createEntryComment(String userId, long partId, UserComment newComment) {
Entry entry = dao.get(partId);
if (entry == null) return null;
authorization.canRead(userId, entry);
Account account = accountController.getByEmail(userId);
Comment comment = new Comment();
comment.setAccount(account);
comment.setEntry(entry);
comment.setBody(newComment.getMessage());
comment.setCreationTime(new Date());
comment = commentDAO.create(comment);
if (newComment.getSamples() != null) {
SampleDAO sampleDAO = DAOFactory.getSampleDAO();
for (PartSample partSample : newComment.getSamples()) {
Sample sample = sampleDAO.get(partSample.getId());
if (sample == null) continue;
comment.getSamples().add(sample);
sample.getComments().add(comment);
}
}
comment = commentDAO.update(comment);
return comment.toDataTransferObject();
}
public boolean deleteHistory(String userId, long entryId, long historyId) {
Entry entry = dao.get(entryId);
if (entry == null) return false;
authorization.expectWrite(userId, entry);
Audit audit = auditDAO.get(historyId);
if (audit == null) return true;
auditDAO.delete(audit);
return true;
}
public ArrayList<UserComment> retrieveEntryComments(String userId, long partId) {
Entry entry = dao.get(partId);
if (entry == null) return null;
authorization.expectRead(userId, entry);
// comments
ArrayList<Comment> comments = commentDAO.retrieveComments(entry);
ArrayList<UserComment> userComments = new ArrayList<>();
for (Comment comment : comments) {
userComments.add(comment.toDataTransferObject());
}
return userComments;
}
public ArrayList<History> getHistory(String userId, long entryId) {
Entry entry = dao.get(entryId);
if (entry == null) return null;
authorization.expectWrite(userId, entry);
List<Audit> list = auditDAO.getAuditsForEntry(entry);
ArrayList<History> result = new ArrayList<>();
for (Audit audit : list) {
History history = audit.toDataTransferObject();
if (history.isLocalUser()) {
history.setAccount(
accountController.getByEmail(history.getUserId()).toDataTransferObject());
}
result.add(history);
}
return result;
}
public boolean deleteTraceSequence(String userId, long entryId, long traceId) {
Entry entry = dao.get(entryId);
if (entry == null) return false;
TraceSequenceDAO traceSequenceDAO = DAOFactory.getTraceSequenceDAO();
TraceSequence traceSequence = traceSequenceDAO.get(traceId);
if (traceSequence == null || !canEdit(userId, traceSequence.getDepositor(), entry))
return false;
try {
new SequenceAnalysisController().removeTraceSequence(traceSequence);
} catch (Exception e) {
Logger.error(e);
return false;
}
return true;
}
public UserComment updateEntryComment(
String userId, long partId, long commentId, UserComment userComment) {
Entry entry = dao.get(partId);
if (entry == null) return null;
authorization.canRead(userId, entry);
Comment comment = commentDAO.get(commentId);
if (comment == null) return createEntryComment(userId, partId, userComment);
if (comment.getEntry().getId() != partId) return null;
if (userComment.getMessage() == null || userComment.getMessage().isEmpty()) return null;
comment.setBody(userComment.getMessage());
comment.setModificationTime(new Date());
return commentDAO.update(comment).toDataTransferObject();
}
public long updatePart(String userId, long partId, PartData part) {
Entry existing = dao.get(partId);
authorization.expectWrite(userId, existing);
Entry entry = InfoToModelFactory.updateEntryField(part, existing);
entry.getLinkedEntries().clear();
if (part.getLinkedParts() != null && part.getLinkedParts().size() > 0) {
for (PartData data : part.getLinkedParts()) {
Entry linked = dao.getByPartNumber(data.getPartId());
// check permissions on link
if (!authorization.canRead(userId, linked)) {
continue;
}
if (!canLink(entry, linked)) continue;
entry.getLinkedEntries().add(linked);
}
}
entry.setModificationTime(Calendar.getInstance().getTime());
if (entry.getVisibility() == Visibility.DRAFT.getValue()) {
List<EntryField> invalidFields = EntryUtil.validates(part);
if (invalidFields.isEmpty()) entry.setVisibility(Visibility.OK.getValue());
}
entry = dao.update(entry);
// check pi email
String piEmail = entry.getPrincipalInvestigatorEmail();
if (StringUtils.isNotEmpty(piEmail)) {
Account pi = DAOFactory.getAccountDAO().getByEmail(piEmail);
if (pi != null) {
// add write permission for the PI (method also checks to see if permission already exists)
AccessPermission accessPermission = new AccessPermission();
accessPermission.setArticle(AccessPermission.Article.ACCOUNT);
accessPermission.setArticleId(pi.getId());
accessPermission.setType(AccessPermission.Type.WRITE_ENTRY);
accessPermission.setTypeId(entry.getId());
permissionsController.addPermission(userId, accessPermission);
}
}
return entry.getId();
}
public PartStatistics retrieveEntryStatistics(String userId, long entryId) {
Entry entry = dao.get(entryId);
if (entry == null) return null;
authorization.expectRead(userId, entry);
PartStatistics statistics = new PartStatistics();
statistics.setEntryId(entryId);
statistics.setCommentCount(commentDAO.getCommentCount(entry));
int traceSequenceCount = DAOFactory.getTraceSequenceDAO().getTraceSequenceCount(entry);
statistics.setTraceSequenceCount(traceSequenceCount);
int sampleCount = DAOFactory.getSampleDAO().getSampleCount(entry);
statistics.setSampleCount(sampleCount);
int historyCount = DAOFactory.getAuditDAO().getHistoryCount(entry);
statistics.setHistoryCount(historyCount);
int eddCount = DAOFactory.getExperimentDAO().getExperimentCount(entryId);
statistics.setExperimentalDataCount(eddCount);
return statistics;
}
protected Entry getEntry(String id) {
Entry entry = null;
// check if numeric
try {
entry = dao.get(Long.decode(id));
} catch (NumberFormatException nfe) {
// fine to ignore
}
// check for part Id
if (entry == null) entry = dao.getByPartNumber(id);
// check for global unique id
if (entry == null) entry = dao.getByRecordId(id);
// get by unique name
if (entry == null) return dao.getByUniqueName(id);
return entry;
}
/**
* Moves the specified list of entries to the deleted folder
*
* @param userId unique identifier for user making the request. Must have write access privileges
* on the entries in the list
* @param list unique identifiers for entries
* @return true or false if operation succeeds on all listed entries or not
*/
public boolean moveEntriesToTrash(String userId, ArrayList<PartData> list) {
List<Entry> toTrash = new LinkedList<>();
for (PartData data : list) {
Entry entry = dao.get(data.getId());
if (entry == null || !authorization.canWriteThoroughCheck(userId, entry)) return false;
toTrash.add(entry);
}
// add to bin
try {
for (Entry entry : toTrash) {
entry.setVisibility(Visibility.DELETED.getValue());
dao.update(entry);
}
} catch (DAOException de) {
Logger.error(de);
return false;
}
return true;
}
public boolean addTraceSequence(String userId, long partId, File file, String uploadFileName) {
Entry entry = dao.get(partId);
if (entry == null) return false;
authorization.expectRead(userId, entry);
FileInputStream inputStream;
try {
inputStream = new FileInputStream(file);
} catch (FileNotFoundException e) {
Logger.error(e);
return false;
}
if (uploadFileName.toLowerCase().endsWith(".zip")) {
try (ZipInputStream zis = new ZipInputStream(inputStream)) {
ZipEntry zipEntry;
while (true) {
zipEntry = zis.getNextEntry();
if (zipEntry != null) {
if (!zipEntry.isDirectory() && !zipEntry.getName().startsWith("__MACOSX")) {
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
int c;
while ((c = zis.read()) != -1) {
byteArrayOutputStream.write(c);
}
boolean parsed =
parseTraceSequence(
userId, entry, zipEntry.getName(), byteArrayOutputStream.toByteArray());
if (!parsed) {
String errMsg =
("Could not parse \""
+ zipEntry.getName()
+ "\". Only Fasta, GenBank & ABI files are supported.");
Logger.error(errMsg);
return false;
}
}
} else {
break;
}
}
} catch (IOException e) {
String errMsg = ("Could not parse zip file.");
Logger.error(errMsg);
return false;
}
} else {
try {
boolean parsed =
parseTraceSequence(userId, entry, uploadFileName, IOUtils.toByteArray(inputStream));
if (!parsed) {
String errMsg =
("Could not parse \""
+ uploadFileName
+ "\". Only Fasta, GenBank & ABI files are supported.");
Logger.error(errMsg);
return false;
}
} catch (IOException e) {
Logger.error(e);
return false;
}
}
return true;
}
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;
}