/**
* Determines if the two entries can be linked
*
* @param entry parent in link hierarchy
* @param link child in link hierarchy
* @return true if the two entries can be linked in the hierarchy specified
*/
private boolean canLink(Entry entry, Entry link) {
if (entry == null || link == null || entry.getId() == link.getId()) return false;
if (link.getLinkedEntries().contains(entry)) return false;
EntryType linkedType = EntryType.nameToType(link.getRecordType());
EntryType type = EntryType.nameToType(entry.getRecordType());
if (type == null || linkedType == null) return false;
switch (type) {
case PLASMID:
if (linkedType != type && linkedType != EntryType.PART) return false;
break;
case PART:
if (linkedType != type) return false;
break;
case STRAIN:
if (linkedType != type && linkedType != EntryType.PLASMID && linkedType != EntryType.PART)
return false;
break;
case ARABIDOPSIS:
if (linkedType != type && linkedType != EntryType.PART) return false;
break;
}
return true;
}
public Response postSequenceFile(
String url, String recordId, EntryType entryType, String sequence) {
WebTarget target = client.target("https://" + url).path("/rest/file/sequence");
Invocation.Builder invocationBuilder = target.request(MediaType.APPLICATION_JSON_TYPE);
final FormDataMultiPart multiPart = new FormDataMultiPart();
multiPart.field("file", IOUtils.toInputStream(sequence), MediaType.TEXT_PLAIN_TYPE);
multiPart.field("entryRecordId", recordId);
multiPart.field("entryType", entryType.name());
return invocationBuilder.post(Entity.entity(multiPart, MediaType.MULTIPART_FORM_DATA_TYPE));
}
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;
}