private void renderVisibility(@NotNull Visibility visibility, @NotNull StringBuilder builder) {
if (!modifiers.contains(Modifier.VISIBILITY)) return;
if (normalizedVisibilities) {
visibility = visibility.normalize();
}
if (!showInternalKeyword && visibility == Visibilities.INTERNAL) return;
builder.append(renderKeyword(visibility.toString())).append(" ");
}
private void renderVisibility(Visibility visibility, StringBuilder builder) {
if (!shouldRenderModifiers()) return;
if ("package".equals(visibility.toString())) {
builder.append("public/*package*/ ");
} else {
builder.append(renderKeyword(visibility.toString())).append(" ");
}
}
@Nullable
public static Integer compare(@NotNull Visibility first, @NotNull Visibility second) {
Integer result = first.compareTo(second);
if (result != null) {
return result;
}
Integer oppositeResult = second.compareTo(first);
if (oppositeResult != null) {
return -oppositeResult;
}
return null;
}
private void initializeProperties() {
setProperty(PROP_SOURCE_NAME, "");
setProperty(PROP_TARGET_NAME, "");
setProperty(PROP_SOURCE_VISIBILITY, "");
setProperty(PROP_TARGET_VISIBILITY, "");
setProperty(PROP_SOURCE_MULTIPLICITY, "1..*");
setProperty(PROP_TARGET_MULTIPLICITY, "1..*");
setProperty(PROP_DIRECTION, DIRECTION_TARGET);
String[] direction = {DIRECTION_NONE, DIRECTION_SOURCE, DIRECTION_TARGET, DIRECTION_BOTH};
setPropertyEditor(PROP_DIRECTION, new ListSelectionPropertyEditor(direction));
setPropertyEditor(
PROP_SOURCE_VISIBILITY, new ListSelectionPropertyEditor(Visibility.stringValues()));
setPropertyEditor(
PROP_TARGET_VISIBILITY, new ListSelectionPropertyEditor(Visibility.stringValues()));
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((value == null) ? 0 : value.hashCode());
result = prime * result + ((visibility == null) ? 0 : visibility.hashCode());
return result;
}
private static void checkVisibility(
@NotNull DeclarationDescriptorWithVisibility descriptor,
@NotNull BindingTrace trace,
@NotNull JetSimpleNameExpression referenceExpression,
@NotNull JetScope scopeToCheckVisibility) {
if (!Visibilities.isVisible(
ReceiverValue.IRRELEVANT_RECEIVER,
descriptor,
scopeToCheckVisibility.getContainingDeclaration())) {
Visibility visibility = descriptor.getVisibility();
if (PsiTreeUtil.getParentOfType(referenceExpression, JetImportDirective.class) != null
&& !visibility.mustCheckInImports()) return;
//noinspection ConstantConditions
trace.report(
INVISIBLE_REFERENCE.on(
referenceExpression, descriptor, visibility, descriptor.getContainingDeclaration()));
}
}
/**
* Returns all program element docs that have a visibility greater or equal than the specified
* level
*/
private <T extends ProgramElementDoc> List<T> filterByVisibility(
T[] docs, Visibility visibility) {
if (visibility == Visibility.PRIVATE) return Arrays.asList(docs);
List<T> filtered = new ArrayList<T>();
for (T doc : docs) {
if (Visibility.get(doc).compareTo(visibility) > 0) filtered.add(doc);
}
return filtered;
}
@Nullable
private static Visibility computeVisibilityToInherit(
@NotNull CallableMemberDescriptor memberDescriptor) {
Collection<? extends CallableMemberDescriptor> overriddenDescriptors =
memberDescriptor.getOverriddenDescriptors();
Visibility maxVisibility = findMaxVisibility(overriddenDescriptors);
if (maxVisibility == null) {
return null;
}
if (memberDescriptor.getKind() == CallableMemberDescriptor.Kind.FAKE_OVERRIDE) {
for (CallableMemberDescriptor overridden : overriddenDescriptors) {
// An implementation (a non-abstract overridden member) of a fake override should have the
// maximum possible visibility
if (overridden.getModality() != Modality.ABSTRACT
&& !overridden.getVisibility().equals(maxVisibility)) {
return null;
}
}
return maxVisibility;
}
return maxVisibility.normalize();
}
@Override
public boolean isVisible(
@NotNull ReceiverValue thisObject,
@NotNull DeclarationDescriptorWithVisibility what,
@NotNull DeclarationDescriptor from) {
if (PRIVATE.isVisible(thisObject, what, from)) {
DeclarationDescriptor classDescriptor =
DescriptorUtils.getParentOfType(what, ClassDescriptor.class);
if (classDescriptor != null && thisObject instanceof ClassReceiver) {
return ((ClassReceiver) thisObject).getDeclarationDescriptor().getOriginal()
== classDescriptor.getOriginal();
}
}
return false;
}
static void load(URL u) {
base = u;
try {
loadSystems();
} catch (Exception e) {
MiscUI.user_fatal("Error loading systems.", e);
}
try {
loadJumps();
} catch (Exception e) {
MiscUI.user_fatal("Error loading jumps.", e);
}
try {
loadConstellations();
} catch (Exception e) {
MiscUI.user_error("Error loading constellations.", e);
}
try {
loadRegions();
} catch (Exception e) {
MiscUI.user_error("Error loading regions.", e);
}
try {
loadStations();
} catch (Exception e) {
MiscUI.user_error("Error loading stations.", e);
}
try {
loadIcons();
} catch (Exception e) {
MiscUI.user_error("Error loading icons.", e);
}
try {
loadHelp();
} catch (Exception e) {
MiscUI.user_error("Error loading help.", e);
}
try {
loadBuildNumber();
} catch (Exception e) {
MiscUI.user_error("Error loading build number.", e);
}
if (buildNumber == -1) MiscUI.user_error("Error loading build number.", null);
Visibility.updateVisibles();
}
@Override
public Property getProperty(String key, String name, Visibility visibility) {
if (ID_PROPERTY_NAME.equals(name)) {
return getIdProperty();
} else if (Edge.LABEL_PROPERTY_NAME.equals(name) && this instanceof Edge) {
return getEdgeLabelProperty();
}
for (Property p : getProperties()) {
if (!p.getKey().equals(key)) {
continue;
}
if (!p.getName().equals(name)) {
continue;
}
if (visibility == null) {
return p;
}
if (!visibility.equals(p.getVisibility())) {
continue;
}
return p;
}
return null;
}
@Override
protected boolean isVisible(
@NotNull DeclarationDescriptorWithVisibility what,
@NotNull DeclarationDescriptor from) {
return PROTECTED.isVisible(what, from) && INTERNAL.isVisible(what, from);
}
public Visibility getVisibility() {
return Visibility.valueOf(visibility.getFragment());
}
public void setVisibility(Visibility visibility) {
this.visibility = URI.create("http://imeji.org/terms/visibility#" + visibility.name());
}
public static void main(String[] args) {
Visibility.test();
// Synchronized.test();
// Reordering.test();
}
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 ColumnVisibility visibilityToAccumuloVisibility(Visibility visibility) {
return new ColumnVisibility(visibility.getVisibilityString());
}
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;
}