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;
}
private static Entry setCommon(Entry entry, PartData info) {
if (entry == null || info == null) return null;
if (info.getName() != null) entry.setName(info.getName());
if (info.getSelectionMarkers() != null) {
Set<SelectionMarker> markers = getSelectionMarkers(info.getSelectionMarkers(), entry);
entry.setSelectionMarkers(markers);
}
if (info.getReferences() != null) entry.setReferences(info.getReferences());
if (StringUtils.isBlank(entry.getPartNumber())) entry.setPartNumber(info.getPartId());
Date currentTime = new Date();
if (entry.getCreationTime() == null) entry.setCreationTime(currentTime);
entry.setModificationTime(currentTime);
if (info.getOwnerEmail() != null) {
entry.setOwnerEmail(info.getOwnerEmail());
}
if (info.getOwner() != null) entry.setOwner(info.getOwner());
if (info.getCreatorEmail() != null) {
entry.setCreatorEmail(info.getCreatorEmail());
}
if (info.getCreator() != null) entry.setCreator(info.getCreator());
if (info.getStatus() == null) {
if (StringUtils.isBlank(entry.getStatus())) entry.setStatus("");
} else entry.setStatus(info.getStatus());
if (info.getAlias() != null) entry.setAlias(info.getAlias());
if (info.getBioSafetyLevel() == null) {
if (entry.getBioSafetyLevel() == null) entry.setBioSafetyLevel(0);
} else entry.setBioSafetyLevel(info.getBioSafetyLevel());
if (info.getShortDescription() != null) entry.setShortDescription(info.getShortDescription());
if (info.getLongDescription() != null) entry.setLongDescription(info.getLongDescription());
if (info.getIntellectualProperty() != null)
entry.setIntellectualProperty(info.getIntellectualProperty());
Set<Link> links = getLinks(info.getLinks(), entry);
entry.setLinks(links);
Visibility visibility = info.getVisibility();
if (visibility != null) entry.setVisibility(visibility.getValue());
// checking for null instead of blank since it could be cleared
if (info.getFundingSource() != null) entry.setFundingSource(info.getFundingSource());
if (info.getPrincipalInvestigator() != null)
entry.setPrincipalInvestigator(info.getPrincipalInvestigator());
if (info.getPrincipalInvestigatorEmail() != null)
entry.setPrincipalInvestigatorEmail(info.getPrincipalInvestigatorEmail());
if (info.getKeywords() != null) entry.setKeywords(info.getKeywords());
// parameters
List<Parameter> parameters = getParameters(info.getCustomFields(), entry);
entry.setParameters(parameters);
return entry;
}