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 FolderDetails retrieveVisibleEntries(
String userId, ColumnField field, boolean asc, int start, int limit) {
Set<Entry> results;
FolderDetails details = new FolderDetails();
Account account = accountController.getByEmail(userId);
if (authorization.isAdmin(userId)) {
// no filters
results = dao.retrieveAllEntries(field, asc, start, limit);
} else {
// retrieve groups for account and filter by permission
Set<Group> accountGroups = new HashSet<>(account.getGroups());
GroupController controller = new GroupController();
Group everybodyGroup = controller.createOrRetrievePublicGroup();
accountGroups.add(everybodyGroup);
results = dao.retrieveVisibleEntries(account, accountGroups, field, asc, start, limit);
}
for (Entry entry : results) {
PartData info = ModelToInfoFactory.createTableViewData(userId, entry, false);
details.getEntries().add(info);
}
return details;
}
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();
}
/**
* Retrieves and sets the default values for the entry. Some of these values (e.g. PI, and Funding
* Source) are set by individual users as part of their personal preferences
*
* @param userId Unique identifier for user requesting the values.
* @param type entry type
* @return PartData object with the retrieve part defaults
*/
public PartData getPartDefaults(String userId, EntryType type) {
PartData partData = new PartData(type);
PreferencesController preferencesController = new PreferencesController();
// pi defaults
String value =
preferencesController.getPreferenceValue(
userId, PreferenceKey.PRINCIPAL_INVESTIGATOR.name());
if (value != null) {
Account piAccount = accountController.getByEmail(value);
if (piAccount == null) {
partData.setPrincipalInvestigator(value);
} else {
partData.setPrincipalInvestigator(piAccount.getFullName());
partData.setPrincipalInvestigatorEmail(piAccount.getEmail());
partData.setPrincipalInvestigatorId(piAccount.getId());
}
}
// funding source defaults
value = preferencesController.getPreferenceValue(userId, PreferenceKey.FUNDING_SOURCE.name());
if (value != null) {
partData.setFundingSource(value);
}
// owner and creator details
Account account = accountController.getByEmail(userId);
if (account != null) {
partData.setOwner(account.getFullName());
partData.setOwnerEmail(account.getEmail());
partData.setCreator(partData.getOwner());
partData.setCreatorEmail(partData.getOwnerEmail());
}
// set the entry type defaults
return EntryUtil.setPartDefaults(partData);
}
/**
* Retrieve the number of entries that is visible to a particular user
*
* @param userId user account unique identifier
* @return Number of entries that user with account referenced in the parameter can read.
*/
public long getNumberOfVisibleEntries(String userId) {
Account account = accountController.getByEmail(userId);
if (account == null) return -1;
if (authorization.isAdmin(userId)) {
return dao.getAllEntryCount();
}
Set<Group> accountGroups = new HashSet<>(account.getGroups());
GroupController controller = new GroupController();
Group everybodyGroup = controller.createOrRetrievePublicGroup();
accountGroups.add(everybodyGroup);
return dao.visibleEntryCount(account, accountGroups);
}
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;
}