├── .github └── workflows │ ├── ci.yaml │ ├── notify-deploy-project.yaml │ └── release.yaml ├── .gitignore ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── contributing.md ├── hooks └── build ├── license.txt ├── mvnw ├── mvnw.cmd ├── pom.xml ├── readme.md └── src ├── main ├── java │ └── edu │ │ └── stanford │ │ └── protege │ │ └── webprotege │ │ ├── ApplicationActionHandlerBeansConfiguration.java │ │ ├── ApplicationBeansConfiguration.java │ │ ├── BatchCollector.java │ │ ├── DataFactory.java │ │ ├── DeserializationUtil.java │ │ ├── EntityMatcherBeansConfiguration.java │ │ ├── ExecutorsConfiguration.java │ │ ├── Filter.java │ │ ├── FormBeansConfiguration.java │ │ ├── FormDataBuilderConfiguration.java │ │ ├── HasDispose.java │ │ ├── HasSubject.java │ │ ├── LuceneBeansConfiguration.java │ │ ├── PrimitiveType.java │ │ ├── ProjectActionHandlerBeansConfiguration.java │ │ ├── ProjectBeansConfiguration.java │ │ ├── ProjectIndexBeansConfiguration.java │ │ ├── ReadWriteLockConfig.java │ │ ├── StreamUtils.java │ │ ├── TestHandler.java │ │ ├── TimeUtil.java │ │ ├── WebprotegeBackendMonolithApplication.java │ │ ├── access │ │ ├── AccessManager.java │ │ ├── AccessManagerConfiguration.java │ │ ├── AccessManagerImpl.java │ │ ├── BuiltInCapability.java │ │ ├── BuiltInRole.java │ │ └── ObjectMapperExtraCapabilitiesCustomizer.java │ │ ├── api │ │ ├── ActionExecutor.java │ │ ├── TimestampDeserializer.java │ │ └── TimestampSerializer.java │ │ ├── app │ │ ├── AccountCreationSetting.java │ │ ├── ApplicationDisposablesManager.java │ │ ├── ApplicationHostSupplier.java │ │ ├── ApplicationLocation.java │ │ ├── ApplicationNameSupplier.java │ │ ├── ApplicationPathSupplier.java │ │ ├── ApplicationPortSupplier.java │ │ ├── ApplicationPreferences.java │ │ ├── ApplicationPreferencesStore.java │ │ ├── ApplicationScheme.java │ │ ├── ApplicationSchemeSupplier.java │ │ ├── ApplicationSettings.java │ │ ├── ApplicationSettingsChecker.java │ │ ├── ApplicationSettingsManager.java │ │ ├── DefaultApplicationPreferences.java │ │ ├── GetApplicationSettingsActionHandler.java │ │ ├── GetApplicationSettingsCommandHandler.java │ │ ├── NotificationEmailsSetting.java │ │ ├── PlaceUrl.java │ │ ├── ProjectComponentFactoryImpl.java │ │ ├── ProjectCreationSetting.java │ │ ├── ProjectUploadSetting.java │ │ ├── SetApplicationSettingsAction.java │ │ ├── SetApplicationSettingsActionHandler.java │ │ ├── SetApplicationSettingsCommandHandler.java │ │ └── SetApplicationSettingsResult.java │ │ ├── axiom │ │ ├── AxiomByRenderingComparator.java │ │ ├── AxiomBySubjectComparator.java │ │ ├── AxiomByTypeComparator.java │ │ ├── AxiomComparatorImpl.java │ │ ├── AxiomIRISubjectProvider.java │ │ ├── AxiomSubjectProvider.java │ │ ├── AxiomTypeGroup.java │ │ ├── AxiomTypeOrdering.java │ │ └── DefaultAxiomTypeOrdering.java │ │ ├── axioms │ │ ├── AddAxiomsCommandHandler.java │ │ ├── AddAxiomsDelegateHandler.java │ │ ├── AxiomsDocumentLoader.java │ │ ├── RemoveAxiomsCommandHandler.java │ │ └── RemoveAxiomsDelegateHandler.java │ │ ├── bulkop │ │ ├── AnnotationSimpleMatchingCriteria.java │ │ ├── EditAnnotationValuesActionHandler.java │ │ ├── EditAnnotationsChangeListGenerator.java │ │ ├── EditAnnotationsChangeListGeneratorFactory.java │ │ ├── EditAnnotationsCommandHandler.java │ │ ├── MoveClassesChangeListGenerator.java │ │ ├── MoveClassesChangeListGeneratorFactory.java │ │ ├── MoveEntitiesToParentCommandHandler.java │ │ ├── MoveToParentActionHandler.java │ │ ├── NewAnnotationData.java │ │ ├── Operation.java │ │ ├── SetAnnotationValueActionChangeListGenerator.java │ │ ├── SetAnnotationValueActionChangeListGeneratorFactory.java │ │ ├── SetAnnotationValueActionHandler.java │ │ └── SetAnnotationValueCommandHandler.java │ │ ├── card │ │ ├── CardContentDescriptor.java │ │ ├── CardDescriptor.java │ │ ├── CardDescriptorRepository.java │ │ ├── CardDescriptorRepositoryImpl.java │ │ ├── CardId.java │ │ ├── CustomContentEntityCardContentDescriptor.java │ │ ├── CustomContentId.java │ │ ├── FormCardContentDescriptor.java │ │ ├── GetEntityCardDescriptorsHandler.java │ │ ├── GetEntityCardDescriptorsProjectActionHandler.java │ │ ├── GetEntityCardDescriptorsRequest.java │ │ ├── GetEntityCardDescriptorsResponse.java │ │ └── ProjectCardDescriptorsRecord.java │ │ ├── change │ │ ├── AbstractCreateEntitiesChangeListGenerator.java │ │ ├── ChangeApplicationResult.java │ │ ├── ChangeDescriptionGenerator.java │ │ ├── ChangeGenerationContext.java │ │ ├── ChangeListGenerator.java │ │ ├── ChangeListMinimiser.java │ │ ├── CreateAnnotationPropertiesChangeGenerator.java │ │ ├── CreateAnnotationPropertiesChangeGeneratorFactory.java │ │ ├── CreateClassesChangeGenerator.java │ │ ├── CreateClassesChangeGeneratorFactory.java │ │ ├── CreateDataPropertiesChangeGenerator.java │ │ ├── CreateDataPropertiesChangeGeneratorFactory.java │ │ ├── CreateObjectPropertiesChangeGenerator.java │ │ ├── CreateObjectPropertiesChangeGeneratorFactory.java │ │ ├── FindAndReplaceIRIPrefixChangeGenerator.java │ │ ├── FindAndReplaceIRIPrefixChangeGeneratorFactory.java │ │ ├── FixedChangeListGenerator.java │ │ ├── GetProjectChangesActionHandler.java │ │ ├── GetProjectChangesCommandHandler.java │ │ ├── HasApplyChanges.java │ │ ├── HasGetChangeSubjects.java │ │ ├── HasHighLevelEvents.java │ │ ├── HasProjectChanges.java │ │ ├── OntologyAxiomPair.java │ │ ├── OntologyChangeComparator.java │ │ ├── OntologyChangeIriReplacer.java │ │ ├── OntologyChangeList.java │ │ ├── OntologyChangeSubjectProvider.java │ │ ├── OwlOntologyChangeTranslator.java │ │ ├── OwlOntologyChangeTranslatorVisitor.java │ │ ├── ProjectChange.java │ │ ├── ProjectChangeTimestampComparator.java │ │ ├── ReverseEngineeredChangeDescriptionGenerator.java │ │ ├── ReverseEngineeredChangeDescriptionGeneratorFactory.java │ │ ├── RevertRevisionActionHandler.java │ │ ├── RevertRevisionCommandHandler.java │ │ ├── RevisionReverterChangeListGenerator.java │ │ ├── RevisionReverterChangeListGeneratorFactory.java │ │ ├── SilentChangeListGenerator.java │ │ ├── description │ │ │ ├── AbstractAnnotationChange.java │ │ │ ├── AbstractCreatedProperties.java │ │ │ ├── AbstractMovedProperties.java │ │ │ ├── AddedAnnotation.java │ │ │ ├── AddedIndividualType.java │ │ │ ├── AddedLanguageTag.java │ │ │ ├── AddedParent.java │ │ │ ├── AddedPropertyDomain.java │ │ │ ├── AddedPropertyRange.java │ │ │ ├── AddedRelationship.java │ │ │ ├── AddedSameAs.java │ │ │ ├── ChangedAnnotationProperty.java │ │ │ ├── CreatedAnnotationProperties.java │ │ │ ├── CreatedClasses.java │ │ │ ├── CreatedDataProperties.java │ │ │ ├── CreatedIndividuals.java │ │ │ ├── CreatedObjectProperties.java │ │ │ ├── DeletedEntities.java │ │ │ ├── DeprecatedEntities.java │ │ │ ├── EditedAnnotationValue.java │ │ │ ├── EditedLanguageTag.java │ │ │ ├── EditedRelationshipValue.java │ │ │ ├── MergedEntities.java │ │ │ ├── MovedAnnotationProperties.java │ │ │ ├── MovedClasses.java │ │ │ ├── MovedDataProperties.java │ │ │ ├── MovedObjectProperties.java │ │ │ ├── RemovedAnnotation.java │ │ │ ├── RemovedIndividualType.java │ │ │ ├── RemovedLanguageTag.java │ │ │ ├── RemovedParent.java │ │ │ ├── RemovedPropertyDomain.java │ │ │ ├── RemovedPropertyRange.java │ │ │ ├── RemovedRelationship.java │ │ │ ├── RemovedSameAs.java │ │ │ ├── SetDataPropertyFunctional.java │ │ │ ├── SetObjectPropertyCharacteristic.java │ │ │ ├── StructuredChangeDescription.java │ │ │ ├── SwitchedAnnotationProperty.java │ │ │ ├── SwitchedRelationshipProperty.java │ │ │ ├── UndeprecatedEntities.java │ │ │ ├── UnsetDataPropertyFunctional.java │ │ │ └── UnsetObjectPropertyCharacteristic.java │ │ └── matcher │ │ │ ├── AbstractAxiomMatcher.java │ │ │ ├── AnnotationAssertionChangeMatcher.java │ │ │ ├── CandidateAxiomEdit.java │ │ │ ├── ChangeMatcher.java │ │ │ ├── ChangeSummary.java │ │ │ ├── ClassAssertionAxiomMatcher.java │ │ │ ├── ClassMoveChangeMatcher.java │ │ │ ├── EditedAnnotationAssertionChangeMatcher.java │ │ │ ├── EntityCreationAxiomSubjectProvider.java │ │ │ ├── EntityCreationMatcher.java │ │ │ ├── EntityDeletionMatcher.java │ │ │ ├── FunctionalDataPropertyAxiomChangeMatcher.java │ │ │ ├── MergeEntitiesMatcher.java │ │ │ ├── PropertyAssertionAxiomMatcher.java │ │ │ ├── PropertyDomainAxiomChangeMatcher.java │ │ │ ├── PropertyFiller.java │ │ │ ├── PropertyRangeAxiomChangeMatcher.java │ │ │ ├── SameIndividualAxiomChangeMatcher.java │ │ │ ├── SubClassOfAxiomMatcher.java │ │ │ ├── SubClassOfEditChangeMatcher.java │ │ │ └── SubClassOfWithFreshEntitiesMatcher.java │ │ ├── color │ │ └── Color.java │ │ ├── crud │ │ ├── CannotGenerateFreshEntityIdException.java │ │ ├── ChangeSetEntityCrudSession.java │ │ ├── ConditionalIriPrefix.java │ │ ├── DeleteEntitiesChangeListGenerator.java │ │ ├── DeleteEntitiesChangeListGeneratorFactory.java │ │ ├── DeleteEntityChangeListGenerator.java │ │ ├── EmptyChangeSetEntityCrudSession.java │ │ ├── EntityCrudContext.java │ │ ├── EntityCrudContextFactory.java │ │ ├── EntityCrudKitHandler.java │ │ ├── EntityCrudKitId.java │ │ ├── EntityCrudKitPlugin.java │ │ ├── EntityCrudKitPluginManager.java │ │ ├── EntityCrudKitPrefixSettings.java │ │ ├── EntityCrudKitRegistry.java │ │ ├── EntityIriPrefixCriteriaRewriter.java │ │ ├── EntityIriPrefixResolver.java │ │ ├── EntityShortForm.java │ │ ├── GetEntityCrudKitSettingsActionHandler.java │ │ ├── GetEntityCrudKitsActionHandler.java │ │ ├── GetEntityCrudKitsCommandHandler.java │ │ ├── HasKitId.java │ │ ├── IRIParser.java │ │ ├── IRIPrefixUpdateStrategy.java │ │ ├── PrefixedNameExpander.java │ │ ├── ProjectEntityCrudKitHandlerCache.java │ │ ├── SetEntityCrudKitSettingsActionHandler.java │ │ ├── SetEntityCrudKitSettingsCommandHandler.java │ │ ├── gen │ │ │ ├── GeneratedAnnotationDescriptor.java │ │ │ ├── GeneratedAnnotationsGenerator.java │ │ │ ├── GeneratedAnnotationsSettings.java │ │ │ ├── GeneratedValueDescriptor.java │ │ │ ├── GeneratedValueDescriptorVisitor.java │ │ │ ├── IncrementingPatternDescriptor.java │ │ │ └── IncrementingPatternDescriptorValueGenerator.java │ │ ├── obo │ │ │ ├── CannotGenerateFreshEntityIdForUserException.java │ │ │ ├── OBOIdSession.java │ │ │ ├── OBOIdSuffixEntityCrudKitHandler.java │ │ │ ├── OBOIdSuffixEntityCrudKitHandlerFactory.java │ │ │ └── OBOIdSuffixEntityCrudKitPlugin.java │ │ ├── persistence │ │ │ ├── ProjectEntityCrudKitSettings.java │ │ │ └── ProjectEntityCrudKitSettingsRepository.java │ │ ├── supplied │ │ │ ├── SuppliedNameSuffixEntityCrudKitHandler.java │ │ │ ├── SuppliedNameSuffixEntityCrudKitHandlerFactory.java │ │ │ └── SuppliedNameSuffixEntityCrudKitPlugin.java │ │ └── uuid │ │ │ ├── UuidEntityCrudKitHandler.java │ │ │ ├── UuidEntityCrudKitHandlerFactory.java │ │ │ └── UuidEntityCrudKitPlugin.java │ │ ├── csv │ │ ├── CSVColumnDescriptor.java │ │ ├── CSVGrid.java │ │ ├── CSVGridParser.java │ │ ├── CSVImportDescriptor.java │ │ ├── CSVReaderHandler.java │ │ ├── CSVRow.java │ │ ├── CSVRowImportType.java │ │ ├── ColumnType.java │ │ ├── DocumentId.java │ │ ├── GetCSVGridAction.java │ │ ├── GetCSVGridActionHandler.java │ │ ├── GetCSVGridResult.java │ │ ├── ImportCSVFileAction.java │ │ ├── ImportCSVFileActionHandler.java │ │ ├── ImportCSVFileChangeListGenerator.java │ │ ├── ImportCSVFileChangeListGeneratorFactory.java │ │ └── ImportCSVFileResult.java │ │ ├── diff │ │ ├── DiffElement.java │ │ ├── DiffElementOperationComparator.java │ │ ├── DiffElementRenderer.java │ │ ├── DiffOperation.java │ │ ├── OntologyDiff2OntologyChanges.java │ │ ├── Revision2DiffElementsTranslator.java │ │ └── SameSubjectFilter.java │ │ ├── dispatch │ │ ├── AbstractProjectActionHandler.java │ │ ├── AbstractProjectChangeHandler.java │ │ ├── ActionExecutionException.java │ │ ├── ActionExecutionResult.java │ │ ├── ActionHandler.java │ │ ├── ActionHandlerNotFoundException.java │ │ ├── ActionHandlerRegistry.java │ │ ├── ApplicationActionHandler.java │ │ ├── DispatchServiceExecutor.java │ │ ├── DispatchServiceResultContainer.java │ │ ├── InvalidRequestException.java │ │ ├── ProjectActionHandler.java │ │ ├── ProjectActionHandlerComponent.java │ │ ├── RequestContext.java │ │ ├── RequestValidationResult.java │ │ ├── RequestValidator.java │ │ ├── Result.java │ │ ├── ValidationResult.java │ │ ├── actions │ │ │ ├── AddAxiomsAction.java │ │ │ ├── AddAxiomsResult.java │ │ │ ├── AxiomsSource.java │ │ │ ├── DeleteAxiomsAction.java │ │ │ ├── DeleteAxiomsResult.java │ │ │ ├── GetRevisionAction.java │ │ │ ├── GetRevisionResult.java │ │ │ ├── GetRevisionsAction.java │ │ │ ├── GetRevisionsResult.java │ │ │ ├── SaveEntityChildrenOrderingAction.java │ │ │ └── SaveEntityChildrenOrderingResult.java │ │ ├── handlers │ │ │ ├── AddAxiomsActionHandler.java │ │ │ ├── AddAxiomsChangeListGenerator.java │ │ │ ├── AddAxiomsChangeListGeneratorFactory.java │ │ │ ├── CreateAnnotationPropertiesActionHandler.java │ │ │ ├── CreateClassesActionHandler.java │ │ │ ├── CreateDataPropertiesActionHandler.java │ │ │ ├── CreateObjectPropertiesActionHandler.java │ │ │ ├── DeleteAxiomsActionHandler.java │ │ │ ├── DeleteAxiomsCommandHandler.java │ │ │ ├── DeleteEntitiesActionHandler.java │ │ │ ├── GetOntologyAnnotationsActionHandler.java │ │ │ ├── GetRevisionActionHandler.java │ │ │ ├── GetRevisionsActionHandler.java │ │ │ ├── GetRootOntologyIdActionHandler.java │ │ │ ├── LoadProjectActionHandler.java │ │ │ ├── LoadProjectCommandHandler.java │ │ │ ├── SaveEntityChildrenOrderingActionHandler.java │ │ │ ├── SaveEntityChildrenOrderingCommandHandler.java │ │ │ └── SetOntologyAnnotationsActionHandler.java │ │ ├── impl │ │ │ ├── ActionHandlerRegistryImpl.java │ │ │ ├── ApplicationActionHandlerRegistry.java │ │ │ ├── DispatchServiceExecutorImpl.java │ │ │ └── ProjectActionHandlerRegistry.java │ │ └── validators │ │ │ ├── ApplicationPermissionValidator.java │ │ │ ├── CompositeRequestValidator.java │ │ │ ├── NullValidator.java │ │ │ ├── ProjectPermissionValidator.java │ │ │ ├── UserIsDicussionThreadCreatorValidator.java │ │ │ ├── UserIsProjectOwnerValidator.java │ │ │ └── UserIsSignedInValidator.java │ │ ├── entity │ │ ├── ChangeEntityIRIActionHandler.java │ │ ├── CommentedEntityData.java │ │ ├── CreateAnnotationPropertiesCommandHandler.java │ │ ├── CreateClassesCommandHandler.java │ │ ├── CreateDataPropertiesCommandHandler.java │ │ ├── CreateEntityFromFormDataActionHandler.java │ │ ├── CreateEntityFromFormDataChangeListGenerator.java │ │ ├── CreateEntityFromFormDataChangeListGeneratorFactory.java │ │ ├── CreateEntityFromFormDataCommandHandler.java │ │ ├── CreateNamedIndividualsCommandHandler.java │ │ ├── CreateObjectPropertiesCommandHandler.java │ │ ├── DeclarationParser.java │ │ ├── Entity.java │ │ ├── EntityDisplay.java │ │ ├── EntityLookupRequest.java │ │ ├── EntityLookupResult.java │ │ ├── EntityNameCharType.java │ │ ├── EntityNameUtils.java │ │ ├── EntityNodeIndex.java │ │ ├── EntityNodeRenderer.java │ │ ├── EntityRenamer.java │ │ ├── EntityShortFormsParser.java │ │ ├── EntityTypeGroup.java │ │ ├── FreshEntityIri.java │ │ ├── GetDeprecatedEntitiesActionHandler.java │ │ ├── GetDeprecatedEntitiesCommandHandler.java │ │ ├── GetEntityDirectParentsAction.java │ │ ├── GetEntityDirectParentsActionHandler.java │ │ ├── GetEntityDirectParentsCommandHandler.java │ │ ├── GetEntityDirectParentsResult.java │ │ ├── LookupEntitiesActionHandler.java │ │ ├── LookupEntitiesCommandHandler.java │ │ ├── MergeEntitiesActionHandler.java │ │ ├── MergeEntitiesChangeListGenerator.java │ │ ├── MergeEntitiesChangeListGeneratorFactory.java │ │ ├── MergeEntitiesCommandHandler.java │ │ ├── MergedEntityTreatment.java │ │ ├── RecordEntityChoiceLookupResult.java │ │ ├── SetEntityDeprecatedCommandHandler.java │ │ ├── SetEntityDeprecatedDelegateHandler.java │ │ └── SubjectClosureResolver.java │ │ ├── events │ │ ├── BrowserTextChangedEventComputer.java │ │ ├── EntityDeprecatedChangedEventTranslator.java │ │ ├── EntityHierarchyChangedEventProxy.java │ │ ├── EntityHierarchyChangedEventProxyFactory.java │ │ ├── EntityTagsChangedEventComputer.java │ │ ├── EventTranslator.java │ │ ├── EventTranslatorManager.java │ │ ├── EventTranslatorSessionAlreadyInProgressException.java │ │ ├── EventTranslatorSessionChecker.java │ │ ├── EventTranslatorSessionId.java │ │ ├── EventTranslatorSessionMismatchException.java │ │ ├── EventTranslatorSessionNotInProgressException.java │ │ ├── HierarchyChangesComputerFactory.java │ │ ├── HighLevelEventGenerator.java │ │ ├── HighLevelProjectEventProxy.java │ │ ├── ManagedHierarchiesChangedComputer.java │ │ └── SimpleHighLevelProjectEventProxy.java │ │ ├── filemanager │ │ ├── ConfigDirectorySupplier.java │ │ ├── ConfigInputStreamSupplier.java │ │ └── FileContents.java │ │ ├── filter │ │ ├── Filter.java │ │ ├── FilterId.java │ │ ├── FilterSet.java │ │ └── FilterSetting.java │ │ ├── forms │ │ ├── AxiomTemplatesParser.java │ │ ├── BindingValuesExtractor.java │ │ ├── ChoiceDescriptorCache.java │ │ ├── ChoiceDescriptorDtoSupplier.java │ │ ├── CopyFormDescriptorsAction.java │ │ ├── CopyFormDescriptorsActionHandler.java │ │ ├── CopyFormDescriptorsCommandHandler.java │ │ ├── CopyFormDescriptorsResult.java │ │ ├── CreateEntityFromFormDataAction.java │ │ ├── CreateEntityFromFormDataResult.java │ │ ├── DeleteFormAction.java │ │ ├── DeleteFormActionHandler.java │ │ ├── DeleteFormCommandHandler.java │ │ ├── DeleteFormResult.java │ │ ├── DeprecateEntityByFormAction.java │ │ ├── DeprecateEntityByFormActionHandler.java │ │ ├── DeprecateEntityByFormChangeListGenerator.java │ │ ├── DeprecateEntityByFormChangeListGeneratorFactory.java │ │ ├── DeprecateEntityByFormResult.java │ │ ├── DynamicListChoiceDescriptorDtoSupplier.java │ │ ├── EntityFormChangeListGenerator.java │ │ ├── EntityFormChangeListGeneratorFactory.java │ │ ├── EntityFormDataRequestSpec.java │ │ ├── EntityFormDescriptor.java │ │ ├── EntityFormManager.java │ │ ├── EntityFormRepository.java │ │ ├── EntityFormRepositoryImpl.java │ │ ├── EntityFormSelector.java │ │ ├── EntityFormSelectorRepository.java │ │ ├── EntityFormSelectorRepositoryImpl.java │ │ ├── EntityFormSubjectFactory.java │ │ ├── EntityFrameFormDataComponent.java │ │ ├── EntityFrameFormDataDtoBuilder.java │ │ ├── EntityFrameFormDataDtoBuilderFactory.java │ │ ├── EntityFrameFormDataDtoBuilderFactoryImpl.java │ │ ├── EntityFrameMapper.java │ │ ├── EntityFrameMapperFactory.java │ │ ├── EntityNameControlValuesBuilder.java │ │ ├── ExpansionState.java │ │ ├── FilterState.java │ │ ├── FixedListChoiceDescriptorDtoSupplier.java │ │ ├── FormControlDataLangTagBasedInclusion.java │ │ ├── FormControlValueDeserializer.java │ │ ├── FormDataBuilderSession.java │ │ ├── FormDataBuilderSessionRenderer.java │ │ ├── FormDataByFormId.java │ │ ├── FormDataUpdateSanityChecker.java │ │ ├── FormDescriptor.java │ │ ├── FormDescriptorDto.java │ │ ├── FormDescriptorDtoTranslator.java │ │ ├── FormDescriptorDtoTranslatorComponent.java │ │ ├── FormDescriptorRecord.java │ │ ├── FormFieldBindingMissingException.java │ │ ├── FormFilterMatcherFactory.java │ │ ├── FormFrame.java │ │ ├── FormFrameBuilder.java │ │ ├── FormFrameConverter.java │ │ ├── FormFrameFlattener.java │ │ ├── FormGroup.java │ │ ├── FormGroupId.java │ │ ├── FormId.java │ │ ├── FormPageRequest.java │ │ ├── FormPageRequestIndex.java │ │ ├── FormPurpose.java │ │ ├── FormRegionAccessRestriction.java │ │ ├── FormRegionCapability.java │ │ ├── FormRegionFilterIndex.java │ │ ├── FormRegionFilterPredicateManager.java │ │ ├── FormRegionOrderingIndex.java │ │ ├── FormRegionPageRequest.java │ │ ├── FormSubjectFactoryDescriptor.java │ │ ├── FormSubjectFactoryDescriptorMissingException.java │ │ ├── FormSubjectResolver.java │ │ ├── FormSubjectTranslator.java │ │ ├── FormsCopier.java │ │ ├── FormsCopierFactory.java │ │ ├── GetEntityCreationFormsAction.java │ │ ├── GetEntityCreationFormsActionHandler.java │ │ ├── GetEntityCreationFormsCommandHandler.java │ │ ├── GetEntityCreationFormsResult.java │ │ ├── GetEntityDeprecationFormsAction.java │ │ ├── GetEntityDeprecationFormsActionHandler.java │ │ ├── GetEntityDeprecationFormsCommandHandler.java │ │ ├── GetEntityDeprecationFormsResult.java │ │ ├── GetEntityFormDescriptorAction.java │ │ ├── GetEntityFormDescriptorActionHandler.java │ │ ├── GetEntityFormDescriptorCommandHandler.java │ │ ├── GetEntityFormDescriptorResult.java │ │ ├── GetEntityFormsAction.java │ │ ├── GetEntityFormsActionHandler.java │ │ ├── GetEntityFormsCommandHandler.java │ │ ├── GetEntityFormsResult.java │ │ ├── GetFormRegionAccessRestrictionsHandler.java │ │ ├── GetFormRegionAccessRestrictionsRequest.java │ │ ├── GetFormRegionAccessRestrictionsResponse.java │ │ ├── GetProjectFormDescriptorsAction.java │ │ ├── GetProjectFormDescriptorsActionHandler.java │ │ ├── GetProjectFormDescriptorsCommandHandler.java │ │ ├── GetProjectFormDescriptorsResult.java │ │ ├── GridColumnBindingMissingException.java │ │ ├── GridControlValuesBuilder.java │ │ ├── HasFilterState.java │ │ ├── HasFormRegionId.java │ │ ├── HasFormRegionPagedChangedHandler.java │ │ ├── ImageControlValuesBuilder.java │ │ ├── MultiChoiceControlValueBuilder.java │ │ ├── NumberControlValuesBuilder.java │ │ ├── OWLEntity2FormControlDataVisitor.java │ │ ├── OWLPrimitive2FormControlDataConverter.java │ │ ├── PrimitiveFormControlDataDtoRenderer.java │ │ ├── PropertyNames.java │ │ ├── PropertyValueFormDataTranslator.java │ │ ├── RegionPageChangedHandler.java │ │ ├── SetEntityFormDescriptorAction.java │ │ ├── SetEntityFormDescriptorActionHandler.java │ │ ├── SetEntityFormDescriptorCommandHandler.java │ │ ├── SetEntityFormDescriptorResult.java │ │ ├── SetEntityFormsDataAction.java │ │ ├── SetEntityFormsDataActionHandler.java │ │ ├── SetEntityFormsDataCommandHandler.java │ │ ├── SetEntityFormsDataResult.java │ │ ├── SetFormRegionAccessRestrictionsHandler.java │ │ ├── SetFormRegionAccessRestrictionsRequest.java │ │ ├── SetFormRegionAccessRestrictionsResponse.java │ │ ├── SetProjectFormDescriptorsAction.java │ │ ├── SetProjectFormDescriptorsActionHandler.java │ │ ├── SetProjectFormDescriptorsCommandHandler.java │ │ ├── SetProjectFormDescriptorsResult.java │ │ ├── SetProjectFormsCommandHandler.java │ │ ├── SetProjectFormsRequest.java │ │ ├── SetProjectFormsResult.java │ │ ├── SingleChoiceControlValuesBuilder.java │ │ ├── SubFormControlValuesBuilder.java │ │ ├── SuppliedNameTemplateResolver.java │ │ ├── TextControlValuesBuilder.java │ │ ├── UpdateFormDescriptorAction.java │ │ ├── UpdateFormDescriptorActionHandler.java │ │ ├── UpdateFormDescriptorCommandHandler.java │ │ ├── UpdateFormDescriptorResult.java │ │ ├── ValidationStatus.java │ │ ├── data │ │ │ ├── ComplexFormControlValue.java │ │ │ ├── CompositePrimitiveFormControlDataMatchCriteria.java │ │ │ ├── EntityFormControlData.java │ │ │ ├── EntityFormControlDataDto.java │ │ │ ├── EntityFormControlDataMatchCriteria.java │ │ │ ├── EntityNameControlData.java │ │ │ ├── EntityNameControlDataDto.java │ │ │ ├── EntityNameControlDataDtoComparator.java │ │ │ ├── FormControlData.java │ │ │ ├── FormControlDataDto.java │ │ │ ├── FormControlDataDtoComparator.java │ │ │ ├── FormControlDataDtoVisitorEx.java │ │ │ ├── FormControlDataVisitor.java │ │ │ ├── FormControlDataVisitorEx.java │ │ │ ├── FormData.java │ │ │ ├── FormDataDto.java │ │ │ ├── FormDataDtoComparator.java │ │ │ ├── FormEntitySubject.java │ │ │ ├── FormEntitySubjectDto.java │ │ │ ├── FormFieldAccessMode.java │ │ │ ├── FormFieldData.java │ │ │ ├── FormFieldDataDto.java │ │ │ ├── FormRegionFilter.java │ │ │ ├── FormSubject.java │ │ │ ├── FormSubjectDto.java │ │ │ ├── GridCellData.java │ │ │ ├── GridCellDataDto.java │ │ │ ├── GridCellDataDtoComparator.java │ │ │ ├── GridControlData.java │ │ │ ├── GridControlDataDto.java │ │ │ ├── GridControlDataDtoComparator.java │ │ │ ├── GridRowData.java │ │ │ ├── GridRowDataDto.java │ │ │ ├── GridRowDataDtoComparatorFactory.java │ │ │ ├── GridRowDtoByColumnIndexComparator.java │ │ │ ├── ImageControlData.java │ │ │ ├── ImageControlDataDto.java │ │ │ ├── ImageControlDataDtoComparator.java │ │ │ ├── IriFormControlData.java │ │ │ ├── IriFormControlDataDto.java │ │ │ ├── LiteralFormControlData.java │ │ │ ├── LiteralFormControlDataDto.java │ │ │ ├── LiteralFormControlDataMatchCriteria.java │ │ │ ├── MultiChoiceControlData.java │ │ │ ├── MultiChoiceControlDataDto.java │ │ │ ├── MultiChoiceControlDataDtoComparator.java │ │ │ ├── NumberControlData.java │ │ │ ├── NumberControlDataDto.java │ │ │ ├── NumberControlDataDtoComparator.java │ │ │ ├── PrimitiveFormControlData.java │ │ │ ├── PrimitiveFormControlData2ProxyConverter.java │ │ │ ├── PrimitiveFormControlDataDto.java │ │ │ ├── PrimitiveFormControlDataMatchCriteria.java │ │ │ ├── PrimitiveFormControlDataMatchCriteriaVisitor.java │ │ │ ├── PrimitiveFormControlDataProxy.java │ │ │ ├── Proxy2PrimitiveFormControlDataConverter.java │ │ │ ├── SimpleFormControlValue.java │ │ │ ├── SingleChoiceControlData.java │ │ │ ├── SingleChoiceControlDataDto.java │ │ │ ├── SingleChoiceControlDataDtoComparator.java │ │ │ ├── TextControlData.java │ │ │ ├── TextControlDataDto.java │ │ │ └── TextControlDataDtoComparator.java │ │ ├── field │ │ │ ├── BoundControlDescriptor.java │ │ │ ├── ChoiceDescriptor.java │ │ │ ├── ChoiceDescriptorDto.java │ │ │ ├── ChoiceListSourceDescriptor.java │ │ │ ├── CompositeFieldDescriptorEntry.java │ │ │ ├── DynamicChoiceListSourceDescriptor.java │ │ │ ├── EntityNameControlDescriptor.java │ │ │ ├── EntityNameControlDescriptorDto.java │ │ │ ├── FieldRun.java │ │ │ ├── FixedChoiceListSourceDescriptor.java │ │ │ ├── FormControlDescriptor.java │ │ │ ├── FormControlDescriptorDto.java │ │ │ ├── FormControlDescriptorDtoVisitor.java │ │ │ ├── FormControlDescriptorVisitor.java │ │ │ ├── FormFieldDeprecationStrategy.java │ │ │ ├── FormFieldDescriptor.java │ │ │ ├── FormFieldDescriptorDto.java │ │ │ ├── FormRegionId.java │ │ │ ├── FormRegionOrdering.java │ │ │ ├── FormRegionOrderingDirection.java │ │ │ ├── FormRegionPresenter.java │ │ │ ├── GridColumnDescriptor.java │ │ │ ├── GridColumnDescriptorDto.java │ │ │ ├── GridControlDescriptor.java │ │ │ ├── GridControlDescriptorDto.java │ │ │ ├── HasRepeatability.java │ │ │ ├── ImageControlDescriptor.java │ │ │ ├── ImageControlDescriptorDto.java │ │ │ ├── LineMode.java │ │ │ ├── MultiChoiceControlDescriptor.java │ │ │ ├── MultiChoiceControlDescriptorDto.java │ │ │ ├── NodeType.java │ │ │ ├── NumberControlDescriptor.java │ │ │ ├── NumberControlDescriptorDto.java │ │ │ ├── NumberControlRange.java │ │ │ ├── NumberControlType.java │ │ │ ├── Optionality.java │ │ │ ├── OwlBinding.java │ │ │ ├── OwlClassBinding.java │ │ │ ├── OwlInstanceBinding.java │ │ │ ├── OwlPropertyBinding.java │ │ │ ├── OwlSubClassBinding.java │ │ │ ├── Repeatability.java │ │ │ ├── SingleChoiceControlDescriptor.java │ │ │ ├── SingleChoiceControlDescriptorDto.java │ │ │ ├── SingleChoiceControlType.java │ │ │ ├── StringType.java │ │ │ ├── SubFormControlDescriptor.java │ │ │ ├── SubFormControlDescriptorDto.java │ │ │ ├── TextControlDescriptor.java │ │ │ └── TextControlDescriptorDto.java │ │ └── processor │ │ │ ├── FormControlDataProcessor.java │ │ │ ├── FormDataConverter.java │ │ │ ├── FormDataProcessor.java │ │ │ ├── FormFieldProcessor.java │ │ │ ├── GridCellDataProcessor.java │ │ │ ├── GridControlDataProcessor.java │ │ │ └── GridRowDataProcessor.java │ │ ├── frame │ │ ├── AbstractUpdateFrameHandler.java │ │ ├── CheckManchesterSyntaxFrameActionHandler.java │ │ ├── CheckManchesterSyntaxFrameCommandHandler.java │ │ ├── ClassFrameProvider.java │ │ ├── ClassFrameProviderImpl.java │ │ ├── ClassFrameTranslationOptions.java │ │ ├── EmptyEntityFrameFactory.java │ │ ├── EntityFrameProvider.java │ │ ├── FrameChangeGenerator.java │ │ ├── FrameChangeGeneratorFactory.java │ │ ├── FrameComponentRenderer.java │ │ ├── FrameComponentRendererImpl.java │ │ ├── FrameComponentSessionRenderer.java │ │ ├── FrameComponentSessionRendererFactory.java │ │ ├── GetAnnotationPropertyFrameActionHandler.java │ │ ├── GetAnnotationPropertyFrameCommandHandler.java │ │ ├── GetClassFrameActionHandler.java │ │ ├── GetClassFrameCommandHandler.java │ │ ├── GetDataPropertyFrameActionHandler.java │ │ ├── GetDataPropertyFrameCommandHandler.java │ │ ├── GetManchesterSyntaxFrameAction.java │ │ ├── GetManchesterSyntaxFrameActionHandler.java │ │ ├── GetManchesterSyntaxFrameCommandHandler.java │ │ ├── GetManchesterSyntaxFrameCompletionsAction.java │ │ ├── GetManchesterSyntaxFrameCompletionsActionHandler.java │ │ ├── GetManchesterSyntaxFrameCompletionsCommandHandler.java │ │ ├── GetManchesterSyntaxFrameCompletionsResult.java │ │ ├── GetManchesterSyntaxFrameResult.java │ │ ├── GetNamedIndividualFrameActionHandler.java │ │ ├── GetNamedIndividualFrameCommandHandler.java │ │ ├── GetObjectPropertyFrameActionHandler.java │ │ ├── GetObjectPropertyFrameCommandHandler.java │ │ ├── GetOntologyFramesActionHandler.java │ │ ├── GetOntologyFramesCommandHandler.java │ │ ├── ManchesterSyntaxFrameParseError.java │ │ ├── ManchesterSyntaxFrameParseResult.java │ │ ├── PlainFrameRenderer.java │ │ ├── PropertyValueDescriptor.java │ │ ├── PropertyValueMinimiser.java │ │ ├── PropertyValueSubsumptionChecker.java │ │ ├── RelationshipTranslationOptions.java │ │ ├── SetManchesterSyntaxFrameAction.java │ │ ├── SetManchesterSyntaxFrameActionHandler.java │ │ ├── SetManchesterSyntaxFrameCommandHandler.java │ │ ├── SetManchesterSyntaxFrameException.java │ │ ├── SetManchesterSyntaxFrameResult.java │ │ ├── State.java │ │ ├── StructuralPropertyValueSubsumptionChecker.java │ │ ├── UpdateAnnotationPropertyFrameActionHandler.java │ │ ├── UpdateAnnotationPropertyFrameCommandHandler.java │ │ ├── UpdateClassFrameActionHandler.java │ │ ├── UpdateClassFrameCommandHandler.java │ │ ├── UpdateDataPropertyFrameCommandHandler.java │ │ ├── UpdateDataPropertyFrameHandler.java │ │ ├── UpdateNamedIndividualFrameCommandHandler.java │ │ ├── UpdateNamedIndividualFrameHandler.java │ │ ├── UpdateObjectPropertyFrameCommandHandler.java │ │ ├── UpdateObjectPropertyFrameHandler.java │ │ └── translator │ │ │ ├── Annotation2PropertyValueTranslator.java │ │ │ ├── Annotation2PropertyValueTranslatorFactory.java │ │ │ ├── AnnotationAssertionAxiom2PropertyValuesTranslator.java │ │ │ ├── AnnotationPropertyFrameTranslator.java │ │ │ ├── Axiom2PropertyValuesTranslator.java │ │ │ ├── AxiomPropertyValueTranslator.java │ │ │ ├── AxiomTranslatorFactory.java │ │ │ ├── Class2ClassFrameTranslator.java │ │ │ ├── Class2ClassFrameTranslatorFactory.java │ │ │ ├── ClassAssertionAxiom2PropertyValuesTranslator.java │ │ │ ├── ClassExpression2PropertyValuesTranslator.java │ │ │ ├── ClassFrame2FrameAxiomsTranslator.java │ │ │ ├── DataPropertyAssertionAxiom2PropertyValuesTranslator.java │ │ │ ├── DataPropertyFrameTranslator.java │ │ │ ├── EquivalentClassesAxiom2PropertyValuesTranslator.java │ │ │ ├── NamedIndividualFrameTranslator.java │ │ │ ├── ObjectPropertyAssertionAxiom2PropertyValuesTranslator.java │ │ │ ├── ObjectPropertyFrameTranslator.java │ │ │ ├── PropertyValue2AxiomTranslator.java │ │ │ ├── PropertyValueTranslator.java │ │ │ └── SubClassOfAxiom2PropertyValuesTranslator.java │ │ ├── hierarchy │ │ ├── AbstractHierarchyProvider.java │ │ ├── AbstractOWLPropertyHierarchyProvider.java │ │ ├── AddEdge.java │ │ ├── AddNamedHierarchyActionHandler.java │ │ ├── AddNamedHierarchyCommandHandler.java │ │ ├── AddRootNode.java │ │ ├── AnnotationPropertyHierarchyProvider.java │ │ ├── AnnotationPropertyHierarchyProviderFactory.java │ │ ├── AnnotationPropertyHierarchyProviderImpl.java │ │ ├── BuiltInHierarchyDescriptors.java │ │ ├── ClassClassAncestorChecker.java │ │ ├── ClassHierarchyProvider.java │ │ ├── ClassHierarchyProviderFactory.java │ │ ├── ClassHierarchyProviderImpl.java │ │ ├── ClassHierarchyRoot.java │ │ ├── ClassHierarchyRootProvider.java │ │ ├── DataPropertyDataPropertyAncestorChecker.java │ │ ├── DataPropertyHierarchyProvider.java │ │ ├── DataPropertyHierarchyProviderFactory.java │ │ ├── DataPropertyHierarchyProviderImpl.java │ │ ├── DataPropertyHierarchyRoot.java │ │ ├── DataPropertyHierarchyRootProvider.java │ │ ├── DropType.java │ │ ├── EdgeChange.java │ │ ├── GetEntityHierarchyChildrenActionHandler.java │ │ ├── GetHierarchyChildrenCommandHandler.java │ │ ├── GetHierarchyDescriptorActionHandler.java │ │ ├── GetHierarchyDescriptorCommandHandler.java │ │ ├── GetHierarchyDescriptorRequest.java │ │ ├── GetHierarchyDescriptorResponse.java │ │ ├── GetHierarchyDescriptorRulesCommandHandler.java │ │ ├── GetHierarchyPathsToRootActionHandler.java │ │ ├── GetHierarchyPathsToRootCommandHandler.java │ │ ├── GetHierarchyRootsActionHandler.java │ │ ├── GetHierarchyRootsCommandHandler.java │ │ ├── GetHierarchySiblingsActionHandler.java │ │ ├── GetHierarchySiblingsCommandHandler.java │ │ ├── GetProjectHierarchyDescriptorRulesCommandHandler.java │ │ ├── GetProjectHierarchyDescriptorRulesRequest.java │ │ ├── GetProjectHierarchyDescriptorRulesResponse.java │ │ ├── GraphEdge.java │ │ ├── GraphModelChange.java │ │ ├── GraphModelChangeVisitor.java │ │ ├── GraphNode.java │ │ ├── GraphNodeRenderer.java │ │ ├── HasGetAncestors.java │ │ ├── HasHasAncestor.java │ │ ├── HierarchyChangesComputer.java │ │ ├── HierarchyDescriptorRepository.java │ │ ├── HierarchyDescriptorRule.java │ │ ├── HierarchyDescriptorRuleDisplayContextMatcher.java │ │ ├── HierarchyDescriptorRuleSelector.java │ │ ├── HierarchyDescriptorRulesRepository.java │ │ ├── HierarchyDescriptorRulesRepositoryImpl.java │ │ ├── HierarchyId.java │ │ ├── HierarchyProvider.java │ │ ├── HierarchyProviderFactory.java │ │ ├── HierarchyProviderGuard.java │ │ ├── HierarchyProviderManager.java │ │ ├── MoveEntityChangeListGenerator.java │ │ ├── MoveEntityChangeListGeneratorFactory.java │ │ ├── MoveHierarchyNodeActionHandler.java │ │ ├── MoveHierarchyNodeCommandHandler.java │ │ ├── NamedHierarchy.java │ │ ├── NamedHierarchyManager.java │ │ ├── NamedHierarchyManagerImpl.java │ │ ├── NamedHierarchyRecord.java │ │ ├── NamedHierarchyRepository.java │ │ ├── NamedIndividualClassAncestorChecker.java │ │ ├── ObjectPropertyHierarchyProvider.java │ │ ├── ObjectPropertyHierarchyProviderFactory.java │ │ ├── ObjectPropertyHierarchyProviderImpl.java │ │ ├── ObjectPropertyHierarchyRoot.java │ │ ├── ObjectPropertyHierarchyRootProvider.java │ │ ├── ObjectPropertyObjectPropertyAncestorChecker.java │ │ ├── Path.java │ │ ├── PathCollector.java │ │ ├── ProjectHierarchyDescriptorRules.java │ │ ├── RemoveEdge.java │ │ ├── RemoveRootNode.java │ │ ├── SetNamedHierarchiesAction.java │ │ ├── SetNamedHierarchiesResponse.java │ │ ├── SetProjectHierarchyDescriptorRulesCommandHandler.java │ │ ├── SetProjectHierarchyDescriptorRulesRequest.java │ │ ├── SetProjectHierarchyDescriptorRulesResponse.java │ │ ├── UpdateUserObject.java │ │ └── ordering │ │ │ ├── OrderedChildrenDocumentService.java │ │ │ ├── ProcessUploadedSiblingsOrderingAction.java │ │ │ ├── ProcessUploadedSiblingsOrderingCommandHandler.java │ │ │ ├── ProcessUploadedSiblingsOrderingResponse.java │ │ │ ├── ProjectOrderedChildren.java │ │ │ ├── ProjectOrderedChildrenManager.java │ │ │ ├── ProjectOrderedChildrenMapper.java │ │ │ ├── ProjectOrderedChildrenRepository.java │ │ │ ├── ProjectOrderedChildrenRepositoryImpl.java │ │ │ ├── ProjectOrderedChildrenService.java │ │ │ ├── ProjectOrderedChildrenServiceImpl.java │ │ │ └── dtos │ │ │ ├── OrderedChild.java │ │ │ └── OrderedChildren.java │ │ ├── index │ │ ├── AnnotationAssertionAxiomsBySubjectIndex.java │ │ ├── AnnotationAssertionAxiomsByValueIndex.java │ │ ├── AnnotationAssertionAxiomsIndex.java │ │ ├── AnnotationAxiomsByIriReferenceIndex.java │ │ ├── AnnotationPropertyDomainAxiomsIndex.java │ │ ├── AnnotationPropertyRangeAxiomsIndex.java │ │ ├── AxiomsByEntityReferenceIndex.java │ │ ├── AxiomsByReferenceIndex.java │ │ ├── AxiomsByTypeIndex.java │ │ ├── BuiltInEntitiesIndex.java │ │ ├── BuiltInOwlEntitiesIndex.java │ │ ├── BuiltInOwlEntitiesIndexImpl.java │ │ ├── BuiltInSkosEntitiesIndex.java │ │ ├── BuiltInSkosEntitiesIndexImpl.java │ │ ├── ClassAssertionAxiomsByClassIndex.java │ │ ├── ClassAssertionAxiomsByIndividualIndex.java │ │ ├── ClassFrameAxiomsIndex.java │ │ ├── ClassHierarchyChildrenAxiomsIndex.java │ │ ├── DataPropertyAssertionAxiomsBySubjectIndex.java │ │ ├── DataPropertyCharacteristicsIndex.java │ │ ├── DataPropertyDomainAxiomsIndex.java │ │ ├── DataPropertyRangeAxiomsIndex.java │ │ ├── DependentIndex.java │ │ ├── DeprecatedEntitiesByEntityIndex.java │ │ ├── DeprecatedEntitiesIndex.java │ │ ├── DeprecatedEntitiesIndexLuceneImpl.java │ │ ├── DifferentIndividualsAxiomsIndex.java │ │ ├── DisjointClassesAxiomsIndex.java │ │ ├── DisjointDataPropertiesAxiomsIndex.java │ │ ├── DisjointObjectPropertiesAxiomsIndex.java │ │ ├── EntitiesInOntologySignatureByIriIndex.java │ │ ├── EntitiesInOntologySignatureIndex.java │ │ ├── EntitiesInProjectSignatureByIriIndex.java │ │ ├── EntitiesInProjectSignatureIndex.java │ │ ├── EquivalentClassesAxiomsIndex.java │ │ ├── EquivalentDataPropertiesAxiomsIndex.java │ │ ├── EquivalentObjectPropertiesAxiomsIndex.java │ │ ├── Index.java │ │ ├── IndexModule.java │ │ ├── IndexUpdatingService.java │ │ ├── IndividualsByTypeIndex.java │ │ ├── IndividualsIndex.java │ │ ├── IndividualsQueryResult.java │ │ ├── InverseObjectPropertyAxiomsIndex.java │ │ ├── NamedIndividualFrameAxiomIndex.java │ │ ├── ObjectPropertyAssertionAxiomsBySubjectIndex.java │ │ ├── ObjectPropertyCharacteristicsIndex.java │ │ ├── ObjectPropertyDomainAxiomsIndex.java │ │ ├── ObjectPropertyRangeAxiomsIndex.java │ │ ├── OntologyAnnotationsIndex.java │ │ ├── OntologyAnnotationsSignatureIndex.java │ │ ├── OntologyAxiomsIndex.java │ │ ├── OntologyAxiomsSignatureIndex.java │ │ ├── OntologySignatureByTypeIndex.java │ │ ├── OntologySignatureIndex.java │ │ ├── ProjectAnnotationAssertionAxiomsBySubjectIndex.java │ │ ├── ProjectAxiomsSignatureIndex.java │ │ ├── ProjectClassAssertionAxiomsByIndividualIndex.java │ │ ├── ProjectOntologiesIndex.java │ │ ├── ProjectSignatureByTypeIndex.java │ │ ├── ProjectSignatureIndex.java │ │ ├── PropertyAssertionAxiomsBySubjectIndex.java │ │ ├── RootIndex.java │ │ ├── SameIndividualAxiomsIndex.java │ │ ├── SubAnnotationPropertyAxiomsBySubPropertyIndex.java │ │ ├── SubAnnotationPropertyAxiomsBySuperPropertyIndex.java │ │ ├── SubClassOfAxiomsBySubClassIndex.java │ │ ├── SubDataPropertyAxiomsBySubPropertyIndex.java │ │ ├── SubObjectPropertyAxiomsBySubPropertyIndex.java │ │ └── impl │ │ │ ├── AnnotationAssertionAxiomsBySubjectIndexImpl.java │ │ │ ├── AnnotationAssertionAxiomsByValueIndexImpl.java │ │ │ ├── AnnotationAssertionAxiomsIndexWrapperImpl.java │ │ │ ├── AnnotationAxiomsByIriReferenceIndexImpl.java │ │ │ ├── AnnotationPropertyDomainAxiomsIndexImpl.java │ │ │ ├── AnnotationPropertyRangeAxiomsIndexImpl.java │ │ │ ├── AxiomChangeHandler.java │ │ │ ├── AxiomMultimapIndex.java │ │ │ ├── AxiomsByEntityReferenceIndexImpl.java │ │ │ ├── AxiomsByReferenceIndexImpl.java │ │ │ ├── AxiomsByTypeIndexImpl.java │ │ │ ├── ClassAssertionAxiomsByClassIndexImpl.java │ │ │ ├── ClassAssertionAxiomsByIndividualIndexImpl.java │ │ │ ├── ClassFrameAxiomsIndexImpl.java │ │ │ ├── ClassHierarchyChildrenAxiomsIndexImpl.java │ │ │ ├── DataPropertyAssertionAxiomsBySubjectIndexImpl.java │ │ │ ├── DataPropertyCharacteristicsIndexImpl.java │ │ │ ├── DataPropertyDomainAxiomsIndexImpl.java │ │ │ ├── DataPropertyRangeAxiomsIndexImpl.java │ │ │ ├── DeprecatedEntitiesByEntityIndexImpl.java │ │ │ ├── DifferentIndividualsAxiomsIndexImpl.java │ │ │ ├── DisjointClassesAxiomsIndexImpl.java │ │ │ ├── DisjointDataPropertiesAxiomsIndexImpl.java │ │ │ ├── DisjointObjectPropertiesAxiomsIndexImpl.java │ │ │ ├── EntitiesInOntologySignatureByIriIndexImpl.java │ │ │ ├── EntitiesInOntologySignatureIndexImpl.java │ │ │ ├── EntitiesInProjectSignatureByIriIndexImpl.java │ │ │ ├── EntitiesInProjectSignatureIndexImpl.java │ │ │ ├── EquivalentClassesAxiomsIndexImpl.java │ │ │ ├── EquivalentDataPropertiesAxiomsIndexImpl.java │ │ │ ├── EquivalentObjectPropertiesAxiomsIndexImpl.java │ │ │ ├── IndexUpdater.java │ │ │ ├── IndexUpdaterFactory.java │ │ │ ├── IndexedSet.java │ │ │ ├── IndexedSetMultimaps.java │ │ │ ├── IndividualsByTypeIndexImpl.java │ │ │ ├── IndividualsIndexImpl.java │ │ │ ├── InverseObjectPropertyAxiomsIndexImpl.java │ │ │ ├── Key.java │ │ │ ├── KeyValueExtractor.java │ │ │ ├── NamedIndividualFrameAxiomsIndexImpl.java │ │ │ ├── ObjectPropertyAssertionAxiomsBySubjectIndexImpl.java │ │ │ ├── ObjectPropertyCharacteristicsIndexImpl.java │ │ │ ├── ObjectPropertyDomainAxiomsIndexImpl.java │ │ │ ├── ObjectPropertyRangeAxiomsIndexImpl.java │ │ │ ├── OntologyAnnotationsIndexImpl.java │ │ │ ├── OntologyAxiomsIndexImpl.java │ │ │ ├── OntologySignatureByTypeIndexImpl.java │ │ │ ├── OntologySignatureIndexImpl.java │ │ │ ├── ProjectClassAssertionAxiomsByIndividualIndexImpl.java │ │ │ ├── ProjectOntologiesIndexImpl.java │ │ │ ├── ProjectSignatureByTypeIndexImpl.java │ │ │ ├── ProjectSignatureIndexImpl.java │ │ │ ├── PropertyAssertionAxiomsBySubjectIndexImpl.java │ │ │ ├── RootIndexImpl.java │ │ │ ├── SameIndividualAxiomsIndexImpl.java │ │ │ ├── Stats.java │ │ │ ├── SubAnnotationPropertyAxiomsBySubPropertyIndexImpl.java │ │ │ ├── SubAnnotationPropertyAxiomsBySuperPropertyIndexImpl.java │ │ │ ├── SubClassOfAxiomsBySubClassIndexImpl.java │ │ │ ├── SubDataPropertyAxiomsBySubPropertyIndexImpl.java │ │ │ ├── SubObjectPropertyAxiomsBySubPropertyIndexImpl.java │ │ │ └── UpdatableIndex.java │ │ ├── individuals │ │ ├── CreateIndividualsChangeListGenerator.java │ │ ├── CreateIndividualsChangeListGeneratorFactory.java │ │ ├── CreateNamedIndividualsActionHandler.java │ │ ├── GetIndividualsActionHandler.java │ │ ├── GetIndividualsCommandHandler.java │ │ ├── GetIndividualsPageContainingIndividualActionHandler.java │ │ ├── GetIndividualsPageContainingIndividualCommandHandler.java │ │ ├── IndividualRendering.java │ │ └── InstanceRetrievalMode.java │ │ ├── init │ │ ├── CheckDataDirectoryIsReadableAndWritable.java │ │ ├── CheckWebProtegeDataDirectoryExists.java │ │ ├── ConfigurationTask.java │ │ └── WebProtegeConfigurationException.java │ │ ├── inject │ │ ├── ApplicationDataFactory.java │ │ ├── ApplicationExecutorsRegistry.java │ │ ├── ApplicationSingleton.java │ │ ├── ConfigurationTasksModule.java │ │ ├── DataDirectory.java │ │ ├── DataDirectoryProvider.java │ │ ├── ExecutorServiceShutdownTask.java │ │ ├── MailProperties.java │ │ ├── OverridableFile.java │ │ ├── OverridableFileFactory.java │ │ ├── ProjectComponent.java │ │ ├── ProjectComponentImpl.java │ │ ├── ProjectSingleton.java │ │ ├── UploadsDirectory.java │ │ ├── UploadsDirectoryProvider.java │ │ └── project │ │ │ ├── ChangeHistoryFile.java │ │ │ ├── ChangeHistoryFileProvider.java │ │ │ ├── OWLDataFactoryProvider.java │ │ │ ├── ProjectDirectory.java │ │ │ ├── ProjectDirectoryFactory.java │ │ │ ├── ProjectDirectoryProvider.java │ │ │ ├── ProjectModule.java │ │ │ ├── ProjectSpecificUiConfigurationDataDirectory.java │ │ │ ├── ProjectSpecificUiConfigurationDataDirectoryProvider.java │ │ │ ├── RevisionNumberProvider.java │ │ │ ├── RootOntology.java │ │ │ ├── RootOntologyDocument.java │ │ │ └── RootOntologyDocumentProvider.java │ │ ├── issues │ │ ├── AddCommentCommandHandler.java │ │ ├── AddCommentHandler.java │ │ ├── CommentConverter.java │ │ ├── CommentNotificationEmailGenerator.java │ │ ├── CommentNotificationEmailTemplate.java │ │ ├── CommentNotificationEmailer.java │ │ ├── CommentParticipantsExtractor.java │ │ ├── CommentRenderer.java │ │ ├── CreateEntityDiscussionThreadCommandHandler.java │ │ ├── CreateEntityDiscussionThreadHandler.java │ │ ├── DeleteEntityCommentCommandHandler.java │ │ ├── DeleteEntityCommentHandler.java │ │ ├── DiscussionThreadParticipantsExtractor.java │ │ ├── EditCommentActionHandler.java │ │ ├── EditCommentCommandHandler.java │ │ ├── EntityDiscussionThread.java │ │ ├── EntityDiscussionThreadRepository.java │ │ ├── GetCommentedEntitiesActionHandler.java │ │ ├── GetCommentedEntitiesCommandHandler.java │ │ ├── GetEntityDiscussionThreadsCommandHandler.java │ │ ├── GetEntityDiscussionThreadsHandler.java │ │ ├── SetDiscussionThreadStatusCommandHandler.java │ │ ├── SetDiscussionThreadStatusHandler.java │ │ └── mention │ │ │ ├── MentionParser.java │ │ │ └── ParsedMention.java │ │ ├── lang │ │ ├── ActiveLanguagesManager.java │ │ ├── ActiveLanguagesManagerImpl.java │ │ ├── DefaultDisplayNameSettingsFactory.java │ │ ├── DictionaryLanguageUsage.java │ │ ├── DisplayNameSettings.java │ │ ├── GetProjectLangTagsActionHandler.java │ │ ├── GetProjectLangTagsCommandHandler.java │ │ └── LanguageManager.java │ │ ├── locking │ │ ├── ReadWriteLockService.java │ │ └── ReadWriteLockServiceImpl.java │ │ ├── mail │ │ ├── CommentMessageIdGenerator.java │ │ ├── GetEmailAddressActionHandler.java │ │ ├── GetEmailAddressCommandHandler.java │ │ ├── MailPropertiesProvider.java │ │ ├── MessageHeader.java │ │ ├── MessageId.java │ │ ├── MessageIdGenerator.java │ │ ├── MessagingExceptionHandler.java │ │ ├── MessagingExceptionHandlerImpl.java │ │ ├── SendMail.java │ │ ├── SendMailImpl.java │ │ ├── SetEmailAddressActionHandler.java │ │ ├── SetEmailAddressRequestValidator.java │ │ └── WebProtegeMimeMessage.java │ │ ├── mansyntax │ │ ├── AutoCompletionChoice.java │ │ ├── AutoCompletionResult.java │ │ ├── EditorPosition.java │ │ ├── ManchesterSyntaxChangeGenerator.java │ │ ├── ManchesterSyntaxChangeGeneratorFactory.java │ │ ├── ManchesterSyntaxFrameParser.java │ │ ├── OntologyAxiomPairChangeGenerator.java │ │ ├── ShellOntologyChecker.java │ │ ├── ShellOwlOntology.java │ │ ├── WebProtegeOWLEntityChecker.java │ │ └── render │ │ │ ├── AbstractOWLAxiomItemSectionRenderer.java │ │ │ ├── AbstractSectionRenderer.java │ │ │ ├── AnnotationPropertyComparatorImpl.java │ │ │ ├── AnnotationPropertyDomainSectionRenderer.java │ │ │ ├── AnnotationPropertyFrameRenderer.java │ │ │ ├── AnnotationPropertyRangeSectionRenderer.java │ │ │ ├── AnnotationPropertySubPropertyOfSectionRenderer.java │ │ │ ├── AnnotationsSectionRenderer.java │ │ │ ├── Bracketing.java │ │ │ ├── ClassDisjointWithSectionRenderer.java │ │ │ ├── ClassEquivalentToSectionRenderer.java │ │ │ ├── ClassFrameRenderer.java │ │ │ ├── ClassSubClassOfSectionRenderer.java │ │ │ ├── DataPropertyCharacteristicsSectionRenderer.java │ │ │ ├── DataPropertyDisjointWithSectionRenderer.java │ │ │ ├── DataPropertyDomainSectionRenderer.java │ │ │ ├── DataPropertyEquivalentToSectionRenderer.java │ │ │ ├── DataPropertyFrameRenderer.java │ │ │ ├── DataPropertyRangeSectionRenderer.java │ │ │ ├── DataPropertySubPropertyOfSectionRenderer.java │ │ │ ├── DefaultHttpLinkRenderer.java │ │ │ ├── DefaultItemStyleProvider.java │ │ │ ├── DeprecatedEntityChecker.java │ │ │ ├── DeprecatedEntityCheckerImpl.java │ │ │ ├── EntityIRIChecker.java │ │ │ ├── EntityIRICheckerImpl.java │ │ │ ├── FrameRenderer.java │ │ │ ├── FrameSectionRenderer.java │ │ │ ├── GetEntityHtmlRenderingActionHandler.java │ │ │ ├── GetEntityRenderingActionHandler.java │ │ │ ├── HasGetRendering.java │ │ │ ├── HighlightedEntityChecker.java │ │ │ ├── HttpLinkRenderer.java │ │ │ ├── IRIOrdinalProvider.java │ │ │ ├── ImageLinkRenderer.java │ │ │ ├── ItemStyleProvider.java │ │ │ ├── LinkInfo.java │ │ │ ├── LinkRendererPlugin.java │ │ │ ├── LiteralRenderer.java │ │ │ ├── LiteralStyle.java │ │ │ ├── ManchesterSyntaxEntityFrameRenderer.java │ │ │ ├── ManchesterSyntaxObjectRenderer.java │ │ │ ├── MarkdownLiteralRenderer.java │ │ │ ├── NamedIndividualDifferentFromSectionRenderer.java │ │ │ ├── NamedIndividualFactsSectionRenderer.java │ │ │ ├── NamedIndividualFrameRenderer.java │ │ │ ├── NamedIndividualSameAsSectionRenderer.java │ │ │ ├── NamedIndividualTypesSectionRenderer.java │ │ │ ├── NestedAnnotationStyle.java │ │ │ ├── NullDeprecatedEntityChecker.java │ │ │ ├── NullHighlightedEntityChecker.java │ │ │ ├── NullHttpLinkRenderer.java │ │ │ ├── ObjectPropertyCharacteristicsSectionRenderer.java │ │ │ ├── ObjectPropertyDisjointWithSectionRenderer.java │ │ │ ├── ObjectPropertyDomainSectionRenderer.java │ │ │ ├── ObjectPropertyEquivalentToSectionRenderer.java │ │ │ ├── ObjectPropertyFrameRenderer.java │ │ │ ├── ObjectPropertyInverseOfSectionRenderer.java │ │ │ ├── ObjectPropertyRangeSectionRenderer.java │ │ │ ├── ObjectPropertySubPropertyChainSectionRenderer.java │ │ │ ├── ObjectPropertySubPropertyOfRenderer.java │ │ │ ├── OntologyAnnotationsSectionRenderer.java │ │ │ ├── OwlOntologyFacade.java │ │ │ ├── OwlOntologyFacadeFactory.java │ │ │ ├── PlainLinkRenderer.java │ │ │ ├── PrettyPrint.java │ │ │ ├── RenderableFormat.java │ │ │ ├── WikipediaXRefLinkRenderer.java │ │ │ └── mansyntax.css │ │ ├── match │ │ ├── AndMatcher.java │ │ ├── AnnotationMatcher.java │ │ ├── AnnotationPropertyMatcher.java │ │ ├── AnnotationValuesAreNotDisjointMatcher.java │ │ ├── AnnotationValuesAreNotDisjointMatcherFactory.java │ │ ├── AnythingMatcher.java │ │ ├── ConflictingBooleanValuesMatcher.java │ │ ├── ConflictingBooleanValuesMatcherFactory.java │ │ ├── DateIsAfterMatcher.java │ │ ├── DateIsBeforeMatcher.java │ │ ├── EntityAnnotationMatcher.java │ │ ├── EntityAnnotationMatcherFactory.java │ │ ├── EntityFrameMatcher.java │ │ ├── EntityIsDeprecatedMatcher.java │ │ ├── EntityIsDeprecatedMatcherFactory.java │ │ ├── EntityMatcherFactory.java │ │ ├── EntityRelationshipMatcher.java │ │ ├── EntityRelationshipMatcherFactory.java │ │ ├── GetMatchingEntitiesActionHandler.java │ │ ├── GetMatchingEntitiesCommandHandler.java │ │ ├── HierarchyPositionCriteriaMatchableEntityTypesExtractor.java │ │ ├── HierarchyPositionMatcherFactory.java │ │ ├── HierarchyPositionMatchingEngine.java │ │ ├── HierarchyPositionMatchingEngineImpl.java │ │ ├── InstanceOfMatcher.java │ │ ├── InstanceOfMatcherFactory.java │ │ ├── IriAnnotationValueMatcher.java │ │ ├── IriAnnotationsMatcher.java │ │ ├── IriAnnotationsMatcherFactory.java │ │ ├── IriLexicalValueMatcher.java │ │ ├── LangTagIsEmptyMatcher.java │ │ ├── LangTagMatchesMatcher.java │ │ ├── LeafClassMatcher.java │ │ ├── LeafClassMatcherFactory.java │ │ ├── LexicalValueNotInDatatypeSpaceMatcher.java │ │ ├── LiteralAnnotationValueMatcher.java │ │ ├── LiteralInLexicalSpaceMatcher.java │ │ ├── LiteralMatcher.java │ │ ├── LiteralMatcherFactory.java │ │ ├── Matcher.java │ │ ├── MatcherAdapter.java │ │ ├── MatcherFactory.java │ │ ├── MatchingEngine.java │ │ ├── MatchingEngineImpl.java │ │ ├── NonUniqueLangTagsMatcher.java │ │ ├── NonUniqueLangTagsMatcherFactory.java │ │ ├── NotMatcher.java │ │ ├── NotSubClassOfMatcher.java │ │ ├── NotSubClassOfMatcherFactory.java │ │ ├── NumericValueMatcher.java │ │ ├── OrMatcher.java │ │ ├── PropertyValueMatcher.java │ │ ├── RelationshipMatcherFactory.java │ │ ├── RelationshipValueMatcher.java │ │ ├── StringContainsMatcher.java │ │ ├── StringContainsRegexMatchMatcher.java │ │ ├── StringContainsRepeatedWhiteSpaceMatcher.java │ │ ├── StringEndsWithMatcher.java │ │ ├── StringEqualsMatcher.java │ │ ├── StringHasUntrimmedSpaceMatcher.java │ │ ├── StringStartsWithMatcher.java │ │ ├── SubClassOfMatcher.java │ │ └── SubClassOfMatcherFactory.java │ │ ├── merge │ │ ├── AnnotationDiffCalculator.java │ │ ├── AxiomDiffCalculator.java │ │ ├── ComputeProjectMergeAction.java │ │ ├── ComputeProjectMergeActionHandler.java │ │ ├── ComputeProjectMergeCommandHandler.java │ │ ├── ComputeProjectMergeResult.java │ │ ├── Diff.java │ │ ├── MergeData.java │ │ ├── MergeUploadedProjectActionHandler.java │ │ ├── MergeUploadedProjectCommandHandler.java │ │ ├── MergeUploadedProjectResult.java │ │ ├── ModifiedProjectOntologiesCalculator.java │ │ ├── ModifiedProjectOntologiesCalculatorFactory.java │ │ ├── OntologyDiff.java │ │ ├── OntologyDiffCalculator.java │ │ ├── OntologyPatcher.java │ │ └── ProjectOntologiesBuilder.java │ │ ├── merge_add │ │ ├── ExistingOntologyMergeAddAction.java │ │ ├── ExistingOntologyMergeAddActionHandler.java │ │ ├── ExistingOntologyMergeAddResult.java │ │ ├── GetUploadedAndProjectOntologyIdsAction.java │ │ ├── GetUploadedAndProjectOntologyIdsActionHandler.java │ │ ├── GetUploadedAndProjectOntologyIdsCommandHandler.java │ │ ├── GetUploadedAndProjectOntologyIdsResult.java │ │ ├── MergeOntologiesAction.java │ │ ├── MergeOntologiesActionHandler.java │ │ ├── MergeOntologiesCommandHandler.java │ │ ├── MergeOntologiesResult.java │ │ ├── MergeOntologyCalculator.java │ │ └── OntologyMergeAddPatcher.java │ │ ├── msg │ │ ├── MessageFormatter.java │ │ └── OWLMessageFormatter.java │ │ ├── object │ │ ├── OWLClassExpressionSelector.java │ │ ├── OWLDataPropertyExpressionSelector.java │ │ ├── OWLEntitySelector.java │ │ ├── OWLIndividualSelector.java │ │ ├── OWLObjectComparatorImpl.java │ │ ├── OWLObjectPropertyExpressionSelector.java │ │ ├── OWLObjectSelector.java │ │ └── SWRLAtomSelector.java │ │ ├── ontology │ │ ├── GetOntologyAnnotationsCommandHandler.java │ │ ├── GetRootOntologyIdCommandHandler.java │ │ ├── ProcessUploadedOntologiesRequest.java │ │ ├── ProcessUploadedOntologiesResponse.java │ │ └── SetOntologyAnnotationsCommandHandler.java │ │ ├── owlapi │ │ ├── BinaryOWLStorerFactory.java │ │ ├── ConjunctSet.java │ │ ├── HasContainsEntityInSignatureImpl.java │ │ ├── NonCachingDataFactory.java │ │ ├── OWLEntityCreator.java │ │ ├── OWLObjectStringFormatter.java │ │ ├── ProjectAnnotationAssertionAxiomsBySubjectIndexImpl.java │ │ ├── RenameMap.java │ │ ├── RenameMapFactory.java │ │ ├── StringFormatterLiteralRendererImpl.java │ │ └── WebProtegeOWLManager.java │ │ ├── permissions │ │ ├── GetProjectPermissionsActionHandler.java │ │ ├── GetProjectPermissionsCommandHandler.java │ │ ├── PermissionDeniedException.java │ │ ├── ProjectPermissionsManager.java │ │ ├── ProjectPermissionsManagerImpl.java │ │ ├── RebuildPermissionsActionHandler.java │ │ ├── RebuildPermissionsCommandHandler.java │ │ ├── RebuildProjectPermissionsRequest.java │ │ └── RebuildProjectPermissionsResponse.java │ │ ├── persistence │ │ ├── CommentId2StringConverter.java │ │ ├── Converter.java │ │ ├── DbName.java │ │ ├── DocumentConverter.java │ │ ├── DocumentConverterUtil.java │ │ ├── DocumentToOwlEntityConverter.java │ │ ├── EmailAddressReadConverter.java │ │ ├── EmailAddressWriteConverter.java │ │ ├── Indexable.java │ │ ├── IriToStringConverter.java │ │ ├── MentionReadConverter.java │ │ ├── MilestoneReadConverter.java │ │ ├── MilestoneWriteConverter.java │ │ ├── OWLEntityReadConverter.java │ │ ├── OWLEntityWriteConverter.java │ │ ├── OwlEntityToDocumentConverter.java │ │ ├── ProjectId2StringConverter.java │ │ ├── ProjectIdReadConverter.java │ │ ├── ProjectIdWriteConverter.java │ │ ├── Repository.java │ │ ├── String2CommentIdConverter.java │ │ ├── String2ProjectIdConverter.java │ │ ├── String2ThreadIdConverter.java │ │ ├── String2UserIdConverter.java │ │ ├── String2ValueObjectConverter.java │ │ ├── StringToIriConverter.java │ │ ├── ThreadId2StringConverter.java │ │ ├── UserId2StringConverter.java │ │ ├── UserIdReadConverter.java │ │ ├── UserIdWriteConverter.java │ │ └── ValueObject2StringConverter.java │ │ ├── perspective │ │ ├── BuiltInPerspectiveLoader.java │ │ ├── BuiltInPerspectivesProvider.java │ │ ├── EntityTypePerspectiveMapper.java │ │ ├── GetPerspectiveDetailsActionHandler.java │ │ ├── GetPerspectiveDetailsCommandHandler.java │ │ ├── GetPerspectiveLayoutActionHandler.java │ │ ├── GetPerspectiveLayoutCommandHandler.java │ │ ├── GetPerspectivesActionHandler.java │ │ ├── GetPerspectivesCommandHandler.java │ │ ├── PerspectiveDescriptorRepository.java │ │ ├── PerspectiveDescriptorRepositoryImpl.java │ │ ├── PerspectiveLayoutRepository.java │ │ ├── PerspectiveLayoutRepositoryImpl.java │ │ ├── PerspectivesManager.java │ │ ├── PerspectivesManagerImpl.java │ │ ├── ResetPerspectiveLayoutActionHandler.java │ │ ├── ResetPerspectiveLayoutCommandHandler.java │ │ ├── ResetPerspectivesActionHandler.java │ │ ├── ResetPerspectivesCommandHandler.java │ │ ├── SetPerspectiveLayoutActionHandler.java │ │ ├── SetPerspectiveLayoutCommandHandler.java │ │ ├── SetPerspectivesActionHandler.java │ │ └── SetPerspectivesCommandHandler.java │ │ ├── place │ │ ├── DefaultItemTypeMapper.java │ │ ├── Item.java │ │ ├── ItemSelection.java │ │ ├── ItemToken.java │ │ ├── ItemTokenParser.java │ │ ├── ItemTokenizer.java │ │ ├── OWLAnnotationPropertyItem.java │ │ ├── OWLClassItem.java │ │ ├── OWLDataPropertyItem.java │ │ ├── OWLEntityItemParser.java │ │ ├── OWLNamedIndividualItem.java │ │ ├── OWLObjectPropertyItem.java │ │ ├── PlaceKey.java │ │ ├── ProjectViewPlace.java │ │ └── ProjectViewPlaceTokenizer.java │ │ ├── portlet │ │ ├── PortletId.java │ │ └── PortletPluginId.java │ │ ├── project │ │ ├── BuiltInPrefixDeclarations.java │ │ ├── BuiltInPrefixDeclarationsLoader.java │ │ ├── CreateNewProjectAction.java │ │ ├── CreateNewProjectCommandHandler.java │ │ ├── CreateNewProjectResult.java │ │ ├── CreateProjectSagaManager.java │ │ ├── DefaultOntologyIdManager.java │ │ ├── DefaultOntologyIdManagerImpl.java │ │ ├── DormantProjectTime.java │ │ ├── GetAvailableProjectsActionHandler.java │ │ ├── GetAvailableProjectsCommandHandler.java │ │ ├── GetAvailableProjectsWithPermissionAction.java │ │ ├── GetAvailableProjectsWithPermissionActionHandler.java │ │ ├── GetAvailableProjectsWithPermissionCommandHandler.java │ │ ├── GetAvailableProjectsWithPermissionResult.java │ │ ├── GetProjectDetailsAction.java │ │ ├── GetProjectDetailsActionHandler.java │ │ ├── GetProjectDetailsCommandHandler.java │ │ ├── GetProjectDetailsResult.java │ │ ├── GetProjectInfoAction.java │ │ ├── GetProjectInfoActionHandler.java │ │ ├── GetProjectInfoCommandHandler.java │ │ ├── GetProjectInfoResult.java │ │ ├── GetProjectPrefixDeclarationsActionHandler.java │ │ ├── GetProjectPrefixDeclarationsCommandHandler.java │ │ ├── HasProjectId.java │ │ ├── ImportedOntologyMetadata.java │ │ ├── InstantiationMode.java │ │ ├── MoveProjectToTrashAction.java │ │ ├── MoveProjectToTrashActionHandler.java │ │ ├── MoveProjectToTrashCommandHandler.java │ │ ├── MoveProjectToTrashResult.java │ │ ├── NewProjectSettings.java │ │ ├── Ontology.java │ │ ├── PackagedProjectChangeEvent.java │ │ ├── PrefixDeclaration.java │ │ ├── PrefixDeclarations.java │ │ ├── PrefixDeclarationsCsvParser.java │ │ ├── PrefixDeclarationsStore.java │ │ ├── ProjectAccessManager.java │ │ ├── ProjectAccessManagerImpl.java │ │ ├── ProjectAlreadyExistsException.java │ │ ├── ProjectAlreadyRegisteredException.java │ │ ├── ProjectCache.java │ │ ├── ProjectCacheManager.java │ │ ├── ProjectComponentFactory.java │ │ ├── ProjectCreationException.java │ │ ├── ProjectDetails.java │ │ ├── ProjectDetailsManager.java │ │ ├── ProjectDetailsManagerImpl.java │ │ ├── ProjectDetailsRepository.java │ │ ├── ProjectDisposablesManager.java │ │ ├── ProjectDocumentExistsException.java │ │ ├── ProjectDocumentNotFoundException.java │ │ ├── ProjectIdFactory.java │ │ ├── ProjectIdFormatException.java │ │ ├── ProjectInputSource.java │ │ ├── ProjectManager.java │ │ ├── ProjectNotRegisteredException.java │ │ ├── ProjectOntologyManagerLoader.java │ │ ├── ProjectPermissionsInitializer.java │ │ ├── RecentProjectRecord.java │ │ ├── RemoveProjectFromTrashAction.java │ │ ├── RemoveProjectFromTrashActionHandler.java │ │ ├── RemoveProjectFromTrashCommandHandler.java │ │ ├── RemoveProjectFromTrashResult.java │ │ ├── RevisionHistoryReplacer.java │ │ ├── SetProjectPrefixDeclarationsActionHandler.java │ │ ├── SetProjectPrefixDeclarationsCommandHandler.java │ │ ├── UnknownProjectException.java │ │ ├── UploadedOntologiesCache.java │ │ ├── WithProjectId.java │ │ └── chg │ │ │ ├── ChangeManager.java │ │ │ ├── OntologyChangeTranslator.java │ │ │ └── OntologyChangeTranslatorVisitor.java │ │ ├── projectsettings │ │ ├── AllProjectSettings.java │ │ ├── EntityDeprecationSettings.java │ │ ├── GetProjectSettingsAction.java │ │ ├── GetProjectSettingsActionHandler.java │ │ ├── GetProjectSettingsCommandHandler.java │ │ ├── GetProjectSettingsResult.java │ │ ├── ProjectSettings.java │ │ ├── ProjectSettingsChangedHandler.java │ │ ├── SetProjectSettingsAction.java │ │ ├── SetProjectSettingsActionHandler.java │ │ ├── SetProjectSettingsCommandHandler.java │ │ ├── SetProjectSettingsResult.java │ │ ├── SlackIntegrationSettings.java │ │ ├── WebhookSetting.java │ │ └── WebhookSettings.java │ │ ├── renderer │ │ ├── AxiomTypeRenderer.java │ │ ├── ContextRenderer.java │ │ ├── GetEntityHtmlRenderingAction.java │ │ ├── GetEntityHtmlRenderingCommandHandler.java │ │ ├── GetEntityHtmlRenderingResult.java │ │ ├── GetEntityRenderingAction.java │ │ ├── GetEntityRenderingCommandHandler.java │ │ ├── GetEntityRenderingResult.java │ │ ├── HasHtmlBrowserText.java │ │ ├── LiteralLangTagTransformer.java │ │ ├── LiteralLexicalFormTransformer.java │ │ ├── LiteralRenderer.java │ │ ├── ManchesterSyntaxKeywords.java │ │ ├── OWLObjectRendererImpl.java │ │ ├── RenderingManager.java │ │ └── ShortFormAdapter.java │ │ ├── repository │ │ └── ProjectEntitySearchFiltersManager.java │ │ ├── revision │ │ ├── CreateInitialRevisionHistoryRequest.java │ │ ├── CreateInitialRevisionHistoryResponse.java │ │ ├── EntitiesByRevisionCache.java │ │ ├── GetHeadRevisionNumberActionHandler.java │ │ ├── GetHeadRevisionNumberCommandHandler.java │ │ ├── GetRevisionSummariesActionHandler.java │ │ ├── GetRevisionSummariesCommandHandler.java │ │ ├── ProjectChangesManager.java │ │ └── RevisionDetailsExtractor.java │ │ ├── search │ │ ├── EntityNameMatchResult.java │ │ ├── EntityNameMatchType.java │ │ ├── EntityNameMatcher.java │ │ ├── EntitySearchFilter.java │ │ ├── EntitySearchFilterId.java │ │ ├── EntitySearchFilterIndexesManager.java │ │ ├── EntitySearchFilterRepository.java │ │ ├── EntitySearchFilterRepositoryImpl.java │ │ ├── EntitySearchResult.java │ │ ├── EntitySearcher.java │ │ ├── EntitySearcherFactory.java │ │ ├── GetSearchSettingsActionHandler.java │ │ ├── GetSearchSettingsCommandHandler.java │ │ ├── PerformEntitySearchActionHandler.java │ │ ├── PerformEntitySearchCommandHandler.java │ │ ├── PrefixNameMatchType.java │ │ ├── ProjectEntitySearchFiltersManagerImpl.java │ │ ├── ProjectSearchSettings.java │ │ ├── SearchField.java │ │ ├── SearchResultMatch.java │ │ ├── SearchResultMatchPosition.java │ │ ├── SearchType.java │ │ ├── SetSearchSettingsActionHandler.java │ │ └── SetSearchSettingsCommandHandler.java │ │ ├── sharing │ │ ├── GetProjectSharingSettingsActionHandler.java │ │ ├── GetProjectSharingSettingsCommandHandler.java │ │ ├── PersonId.java │ │ ├── ProjectSharingSettings.java │ │ ├── ProjectSharingSettingsManager.java │ │ ├── ProjectSharingSettingsManagerImpl.java │ │ ├── Roles.java │ │ ├── SetProjectSharingSettingsActionHandler.java │ │ ├── SetProjectSharingSettingsCommandHandler.java │ │ ├── SharingPermission.java │ │ └── SharingSetting.java │ │ ├── shortform │ │ ├── AnnotationAssertionAxiomsModule.java │ │ ├── AnnotationAssertionBasedDictionaryLanguage.java │ │ ├── BuiltInShortFormDictionary.java │ │ ├── DefaultShortFormAnnotationPropertyIRIs.java │ │ ├── DeprecatedEntitiesByEntityIndexLuceneImpl.java │ │ ├── DictionaryLanguageFieldWriter.java │ │ ├── DictionaryManager.java │ │ ├── DictionaryUpdatesProcessor.java │ │ ├── EntityAnnotationAssertionsDocumentAugmenter.java │ │ ├── EntityBasedSimilarity.java │ │ ├── EntityBuiltInStatusDocumentAugmenter.java │ │ ├── EntityDictionaryLanguageValues.java │ │ ├── EntityDocumentAugmenter.java │ │ ├── EntityDocumentFieldNames.java │ │ ├── EntityLocalNameDocumentAugmenter.java │ │ ├── EntityOboIdDocumentAugmenter.java │ │ ├── EntityPrefixedNameDocumentAugmenter.java │ │ ├── EntitySearchFilterMatcher.java │ │ ├── EntitySearchFilterMatchersFactory.java │ │ ├── EscapingShortFormProvider.java │ │ ├── FieldNameTranslator.java │ │ ├── FieldNameTranslatorImpl.java │ │ ├── IndexingAnalyzerFactory.java │ │ ├── IndexingAnalyzerWrapper.java │ │ ├── IriShortFormAdapter.java │ │ ├── LocalNameExtractor.java │ │ ├── LocalNameShortFormCache.java │ │ ├── LuceneDictionaryLanguageValuesMatcher.java │ │ ├── LuceneEntityDocument.java │ │ ├── LuceneEntityDocumentTranslator.java │ │ ├── LuceneEntityDocumentTranslatorImpl.java │ │ ├── LuceneIndex.java │ │ ├── LuceneIndexImpl.java │ │ ├── LuceneIndexUpdater.java │ │ ├── LuceneIndexUpdaterImpl.java │ │ ├── LuceneIndexWriter.java │ │ ├── LuceneIndexWriterImpl.java │ │ ├── LuceneIndexesDirectory.java │ │ ├── LuceneModule.java │ │ ├── LuceneMultiLingualDictionaryUpdater.java │ │ ├── LuceneQueryFactory.java │ │ ├── LuceneSearchStringTokenizer.java │ │ ├── MaxGramSize.java │ │ ├── MinGramSize.java │ │ ├── MultiLingualDictionary.java │ │ ├── MultiLingualDictionaryLuceneImpl.java │ │ ├── MultiLingualShortFormDictionary.java │ │ ├── MultiLingualShortFormDictionaryLuceneImpl.java │ │ ├── MultiLingualShortFormIndex.java │ │ ├── MultiLingualShortFormIndexLuceneImpl.java │ │ ├── MultilingualDictionaryUpdater.java │ │ ├── ProjectLuceneDirectoryPathSupplier.java │ │ ├── QueryAnalyzerFactory.java │ │ ├── Scanner.java │ │ ├── SearchFiltersDocumentAugmenter.java │ │ ├── SearchString.java │ │ ├── SearchableMultiLingualShortFormDictionary.java │ │ ├── SearchableMultiLingualShortFormDictionaryLuceneImpl.java │ │ ├── ShortFormCache.java │ │ ├── ShortFormMatchFunction.java │ │ ├── ShortFormQuotingUtils.java │ │ ├── WebProtegeOntologyIRIShortFormProvider.java │ │ └── WellKnownLabellingIris.java │ │ ├── storage │ │ ├── MinioFileDownloader.java │ │ ├── MinioProperties.java │ │ └── StorageException.java │ │ ├── tag │ │ ├── CriteriaBasedTagsManager.java │ │ ├── EntityTags.java │ │ ├── EntityTagsRepository.java │ │ ├── EntityTagsRepositoryImpl.java │ │ ├── GetEntityTagsActionHandler.java │ │ ├── GetEntityTagsCommandHandler.java │ │ ├── GetProjectTagsActionHandler.java │ │ ├── GetProjectTagsCommandHandler.java │ │ ├── SetProjectTagsActionHandler.java │ │ ├── SetProjectTagsCommandHandler.java │ │ ├── Tag.java │ │ ├── TagData.java │ │ ├── TagId.java │ │ ├── TagRepository.java │ │ ├── TagRepositoryImpl.java │ │ ├── TagsManager.java │ │ ├── UpdateEntityTagsActionHandler.java │ │ └── UpdateEntityTagsCommandHandler.java │ │ ├── templates │ │ ├── TemplateEngine.java │ │ └── TemplateObjectsBuilder.java │ │ ├── trigger │ │ ├── Trigger.java │ │ ├── TriggerAction.java │ │ └── TriggerRunner.java │ │ ├── ui │ │ ├── DisplayContext.java │ │ ├── ViewId.java │ │ └── ViewNodeId.java │ │ ├── usage │ │ ├── GetEntityUsageActionHandler.java │ │ ├── GetEntityUsageCommandHandler.java │ │ ├── ReferencingAxiomVisitor.java │ │ ├── ReferencingAxiomVisitorFactory.java │ │ ├── UsageFilter.java │ │ ├── UsageReference.java │ │ └── UsageReferenceComparator.java │ │ ├── user │ │ ├── EmailAddress.java │ │ ├── GetAuthenticatedUserDetailsActionHandler.java │ │ ├── GetAuthenticatedUserDetailsCommandHandler.java │ │ ├── GetUserIdCompletionsAction.java │ │ ├── GetUserIdCompletionsActionHandler.java │ │ ├── GetUserIdCompletionsCommandHandler.java │ │ ├── GetUserIdCompletionsResult.java │ │ ├── UnrecognizedUserNameException.java │ │ ├── UserActivityManager.java │ │ ├── UserActivityManagerProvider.java │ │ ├── UserActivityRecord.java │ │ ├── UserDetails.java │ │ ├── UserDetailsManager.java │ │ ├── UserDetailsManagerConfiguration.java │ │ ├── UserDetailsManagerImpl.java │ │ ├── UserEmailAlreadyExistsException.java │ │ ├── UserIdInitialsExtractor.java │ │ ├── UserIdProjectIdKey.java │ │ ├── UserNameAlreadyExistsException.java │ │ ├── UserRecord.java │ │ ├── UserRecordConverter.java │ │ ├── UserRecordRepository.java │ │ ├── UserRegistrationException.java │ │ ├── UsersQueryRequest.java │ │ └── UsersQueryResponse.java │ │ ├── util │ │ ├── AlphaNumericStringComparator.java │ │ ├── ClassExpression.java │ │ ├── Counter.java │ │ ├── DisposableObjectManager.java │ │ ├── EntityDeleter.java │ │ ├── FileContentsSizeCalculator.java │ │ ├── IdUtil.java │ │ ├── IriReplacer.java │ │ ├── IriReplacerFactory.java │ │ ├── MemoryMonitor.java │ │ ├── Named.java │ │ ├── OWLOntologyChangeDataVisitorAdapter.java │ │ ├── ReferenceFinder.java │ │ ├── TempFileFactory.java │ │ ├── TempFileFactoryImpl.java │ │ └── UUIDUtil.java │ │ ├── viz │ │ ├── AnyEdgeCriteria.java │ │ ├── AnyEdgeTypeCriteria.java │ │ ├── AnyInstanceOfEdgeCriteria.java │ │ ├── AnyNodeCriteria.java │ │ ├── AnyRelationshipEdgeCriteria.java │ │ ├── AnySubClassOfEdgeCriteria.java │ │ ├── CompositeEdgeCriteria.java │ │ ├── DotRenderer.java │ │ ├── DotRendererFactory.java │ │ ├── Edge.java │ │ ├── EdgeCriteria.java │ │ ├── EdgeCriteriaSplitter.java │ │ ├── EdgeCriteriaVisitor.java │ │ ├── EdgeMatcher.java │ │ ├── EdgeMatcherFactory.java │ │ ├── EdgeNodeCriteria.java │ │ ├── EdgeTypeCriteria.java │ │ ├── EntityGraph.java │ │ ├── EntityGraphBuilder.java │ │ ├── EntityGraphBuilderFactory.java │ │ ├── EntityGraphEdgeLimit.java │ │ ├── EntityGraphFilter.java │ │ ├── EntityGraphSettings.java │ │ ├── EntityGraphSettingsRepository.java │ │ ├── EntityGraphSettingsRepositoryImpl.java │ │ ├── FilterName.java │ │ ├── GetEntityGraphActionHandler.java │ │ ├── GetEntityGraphCommandHandler.java │ │ ├── GetUserProjectEntityGraphCriteriaActionHandler.java │ │ ├── GetUserProjectEntityGraphCriteriaCommandHandler.java │ │ ├── HeadNodeMatchesCriteria.java │ │ ├── IsAEdge.java │ │ ├── NegatedEdgeCriteria.java │ │ ├── NoEdgeCriteria.java │ │ ├── NodeMatchesCriteria.java │ │ ├── ProjectUserEntityGraphSettings.java │ │ ├── RelationshipEdge.java │ │ ├── RelationshipEdgePropertyEqualsCriteria.java │ │ ├── SetEntityGraphActiveFiltersActionHandler.java │ │ ├── SetEntityGraphActiveFiltersCommandHandler.java │ │ ├── SetUserProjectEntityGraphCriteriaActionHandler.java │ │ ├── SetUserProjectEntityGraphSettingsCommandHandler.java │ │ ├── SplitEdgeCriteria.java │ │ └── TailNodeMatchesCriteria.java │ │ ├── watches │ │ ├── GetWatchesActionHandler.java │ │ ├── GetWatchesCommandHandler.java │ │ ├── IndirectlyWatchedEntitiesFinder.java │ │ ├── SetWatchesActionHandler.java │ │ ├── SetWatchesCommandHandler.java │ │ ├── Watch.java │ │ ├── WatchManager.java │ │ ├── WatchManagerImpl.java │ │ ├── WatchNotificationEmailTemplate.java │ │ ├── WatchRecord.java │ │ ├── WatchRecordRepository.java │ │ ├── WatchRecordRepositoryImpl.java │ │ ├── WatchTriggeredHandler.java │ │ ├── WatchTriggeredHandlerImpl.java │ │ ├── WatchType.java │ │ └── WatchedChangesManager.java │ │ └── webhook │ │ ├── CommentNotificationSlackTemplate.java │ │ ├── CommentPostedSlackWebhookInvoker.java │ │ ├── JsonPayloadWebhookExecutor.java │ │ ├── PostWebhookPayloadTask.java │ │ ├── ProjectChangedWebhookInvoker.java │ │ ├── ProjectChangedWebhookPayload.java │ │ ├── ProjectWebhook.java │ │ ├── ProjectWebhookEventType.java │ │ ├── SlackWebhook.java │ │ ├── SlackWebhookRepository.java │ │ ├── SlackWebhookRepositoryImpl.java │ │ ├── Webhook.java │ │ ├── WebhookExecutor.java │ │ ├── WebhookInvocation.java │ │ ├── WebhookInvoker.java │ │ ├── WebhookRepository.java │ │ └── WebhookRepositoryImpl.java └── resources │ ├── application-local.properties │ ├── application.properties │ ├── built-in-prefixes.csv │ ├── builtin-perspective-data │ ├── Classes.json │ ├── Comments.json │ ├── History.json │ ├── Individuals.json │ ├── OWL Classes.json │ ├── OWL Properties.json │ ├── Properties.json │ └── Query.json │ ├── logback-spring.xml │ └── templates │ ├── comment-notification-email-template.html │ ├── comment-notification-slack-template.json │ ├── password-reset-email-template.html │ └── watch-notification-email-template.html └── test ├── java └── edu │ └── stanford │ └── protege │ └── webprotege │ ├── DataFactory_TestCase.java │ ├── IndexUpdaterServiceTestConfiguration.java │ ├── MockingUtils.java │ ├── MongoTestExtension.java │ ├── OWLDeclarationAxiomMatcher.java │ ├── OWLEntityMatcher.java │ ├── OWLLiteralWithLexicalValueMatcher.java │ ├── RabbitTestExtension.java │ ├── RdfsLabelWithLexicalValueMatcher.java │ ├── TimeUtil_TestCase.java │ ├── access │ ├── ApplicationResource_TestCase.java │ ├── ObjectMapperExtraCapabilitiesCustomizerTest.java │ ├── ProjectResource_TestCase.java │ ├── RoleId_Json_TestCase.java │ ├── RoleId_TestCase.java │ ├── Subject_AnySignedInUser_TestCase.java │ ├── Subject_GuestUser_TestCase.java │ └── Subject_SpecificUser_TestCase.java │ ├── admin │ ├── ApplicationPreferencesManager_TestCase.java │ ├── ApplicationPreferencesStore_IT.java │ └── GetApplicationPreferencesActionHandler_TestCase.java │ ├── api │ └── TimestampDeserializer_TestCase.java │ ├── axiom │ ├── AxiomByRenderingComparator_TestCase.java │ ├── AxiomBySubjectComparator_TestCase.java │ ├── AxiomByTypeComparator_TestCase.java │ ├── AxiomComparatorImpl_TestCase.java │ ├── AxiomIRISubjectProvider_TestCase.java │ ├── AxiomSubjectProvider_TestCase.java │ └── DefaultAxiomTypeOrdering_TestCase.java │ ├── card │ └── CardDescriptorRepositoryImpl_IT.java │ ├── change │ ├── ChangeApplicationResult_TestCase.java │ ├── ChangeGenerationContext_TestCase.java │ ├── ChangeListMinimiser_TestCase.java │ ├── OntologyChangeList_TestCase.java │ ├── OwlOntologyChangeTranslatorVisitor_TestCase.java │ ├── OwlOntologyChangeTranslator_TestCase.java │ ├── ProjectChangeTimestampComparator_TestCase.java │ └── RevisionReverterChangeListGenerator_TestCase.java │ ├── crud │ ├── EntityIriPrefixResolver_TestCase.java │ ├── HierarchyPositionCriteriaMatchableEntityTypesExtractor_TestCase.java │ ├── IRIParserTestCase.java │ ├── gen │ │ └── IncrementingPatternDescriptorValueGenerator_TestCase.java │ ├── obo │ │ └── OboIdSessionTestCase.java │ ├── supplied │ │ └── SuppliedNameSuffixEntityCrudKitHandlerTestCase.java │ └── uuid │ │ ├── UuidEntityCrudKitHandlerTestCase.java │ │ └── UuidEntityCrudKitPluginTestCase.java │ ├── dispatch │ ├── ActionExecutionResult_TestCase.java │ ├── ExecutionContext_TestCase.java │ ├── impl │ │ ├── ApplicationActionHandlerRegistry_Test.java │ │ └── DispatchServiceExecutorImpl_TestCase.java │ └── validators │ │ └── UserIsSignedInValidator_TestCase.java │ ├── entity │ ├── DeclarationParser_TestCase.java │ ├── EntityNameChar_TestCase.java │ ├── EntityNameUtils_IndexOfWordEnd_TestCase.java │ ├── EntityNameUtils_IndexOfWord_TestCase.java │ ├── EntityNameUtils_IsQuoted_TestCase.java │ ├── EntityNameUtils_IsWordStart_TestCase.java │ ├── FreshEntityIri_TestCase.java │ ├── MergeEntitiesChangeListGenerator_TestCase.java │ └── SubjectClosureResolver_TestCase.java │ ├── events │ ├── EventTranslatorManagerLifeCycleTest.java │ └── EventTranslatorSessionCheckerTest.java │ ├── forms │ ├── AxiomTemplatesParser_IT.java │ ├── CopyFormDescriptorsFromProject_Serialization_TestCase.java │ ├── DeleteForm_Serialization_TestCase.java │ ├── EntityFormRepositoryImpl_IT.java │ ├── EntityFormSelectorRepositoryImpl_IT.java │ ├── FormControlValueDeserializer_TestCase.java │ ├── FormDataByFormIdTest.java │ ├── FormDataConverter_TestCase.java │ ├── FormDataRepository_IT.java │ ├── FormDescriptor_Serialization_IT.java │ ├── FormFieldDescriptor_Serialization_IT.java │ ├── FormFrameFlattener_TestCase.java │ ├── FormId_TestCase.java │ ├── FormSubjectFactoryDescriptorTest.java │ ├── GetEntityCreationForms_Serialization_TestCase.java │ ├── GetEntityDeprecationForms_Serialization_TestCase.java │ ├── GetEntityFormDescriptor_Serialization_TestCase.java │ ├── GetEntityFormsActionHandlerIT.java │ ├── GetEntityForms_Serialization_TestCase.java │ ├── GetProjectFormDescriptors_Serialization_TestCase.java │ ├── UpdateFormDescriptor_Serialization_TestCase.java │ ├── data │ │ ├── EntityNameControlDataDtoTest.java │ │ ├── FormFieldAccessModeTest.java │ │ ├── FormFieldDataDtoTest.java │ │ ├── FormFieldDataTest.java │ │ ├── GridCellDataDtoTest.java │ │ ├── GridControlDataDtoTest.java │ │ ├── GridRowDataDtoComparatorFactory_TestCase.java │ │ ├── GridRowDataDtoTest.java │ │ ├── MultiChoiceControlDataDtoTest.java │ │ ├── PrimitiveFormControlDataDtoTest.java │ │ ├── PrimitiveFormControlDataTest.java │ │ ├── SingleChoiceControlDataDtoTest.java │ │ ├── TextControlDataDtoTest.java │ │ └── TextControlDataTest.java │ ├── field │ │ ├── ChoiceDescriptorTest.java │ │ ├── ChoiceDescriptor_Serialization_TestCase.java │ │ ├── ChoiceListSourceDescriptor_Serialization_TestCase.java │ │ ├── DynamicChoiceListSourceDescriptorTest.java │ │ ├── EntityNameControlDescriptorDtoTest.java │ │ ├── EntityNameControlDescriptorTest.java │ │ ├── FixedChoiceListSourceDescriptorTest.java │ │ ├── FormDescriptorTest.java │ │ ├── FormFieldDescriptorTest.java │ │ ├── FormRegionId_TestCase.java │ │ ├── FormRegionOrdering_TestCase.java │ │ ├── GridColumnDescriptor_Serialization_Test.java │ │ ├── GridControlDescriptor_Serialization_TestCase.java │ │ ├── MultiChoiceControlDescriptor_Serialization_TestCase.java │ │ ├── OwlPropertyBindingTest.java │ │ ├── OwlSubClassBindingTest.java │ │ ├── SingleChoiceControlDescriptor_Serialization_TestCase.java │ │ ├── SubFormControlDescriptor_IT.java │ │ ├── TextControlDescriptorTest.java │ │ └── TextControlDescriptor_TestCase.java │ └── processor │ │ ├── FormControlDataProcessor_TestCase.java │ │ ├── FormDataProcessor_TestCase.java │ │ ├── FormFieldProcessor_TestCase.java │ │ ├── GridCellDataProcessor_TestCase.java │ │ ├── GridControlDataProcessor_TestCase.java │ │ └── GridRowDataProcessor_TestCase.java │ ├── frame │ ├── OwlOntologyFacade_ManchesterSyntaxAxioms_TestCase.java │ └── translator │ │ ├── Annotation2PropertyValueTranslator_TestCase.java │ │ └── ClassExpression2PropertyValuesTranslator_TestCase.java │ ├── hierarchy │ ├── AnnotationPropertyHierarchyProviderImpl_TestCase.java │ ├── ClassHierarchyProviderImpl_TestCase.java │ ├── DataPropertyHierarchyProvider_TestCase.java │ ├── FixedRootClassHierarchyProvider_TestCase.java │ ├── GetHierarchyDescriptorActionHandlerTest.java │ ├── GetHierarchyDescriptorCommandHandlerTest.java │ ├── GetHierarchyDescriptorRequestTest.java │ ├── GetHierarchyDescriptorResponseTest.java │ ├── GetHierarchyDescriptorRulesCommandHandlerTest.java │ ├── GetProjectHierarchyDescriptorRulesRequestTest.java │ ├── GetProjectHierarchyDescriptorRulesResponseTest.java │ ├── HierarchyChangesComputerTest.java │ ├── HierarchyDescriptorRuleDisplayContextMatcherTest.java │ ├── HierarchyDescriptorRuleSelectorTest.java │ ├── HierarchyDescriptorRuleTest.java │ ├── HierarchyDescriptorRulesRepositoryImplIT.java │ ├── HierarchyIdTest.java │ ├── NamedHierarchyJsonTest.java │ ├── NamedHierarchyRepositoryIT.java │ ├── ObjectPropertyHierarchyProviderImpl_TestCase.java │ ├── ProjectHierarchyDescriptorRulesTest.java │ └── ordering │ │ ├── OrderedChildrenDocumentServiceTest.java │ │ ├── ProcessUploadedSiblingsOrderingCommandHandlerIT.java │ │ ├── ProjectOrderedChildrenManagerIT.java │ │ ├── ProjectOrderedChildrenMapperTest.java │ │ └── ProjectOrderedChildrenServiceImplIT.java │ ├── index │ └── impl │ │ ├── AnnotationAssertionAxiomsBySubjectIndexImpl_TestCase.java │ │ ├── AnnotationAssertionAxiomsByValueIndexImpl_TestCase.java │ │ ├── AnnotationAxiomsByIriReferenceIndexImpl_AnnotationAssertionAxiom_TestCase.java │ │ ├── AnnotationAxiomsByIriReferenceIndexImpl_AnnotationPropertyDomain_TestCase.java │ │ ├── AnnotationAxiomsByIriReferenceIndexImpl_AnnotationPropertyRange_TestCase.java │ │ ├── AnnotationPropertyDomainAxiomsIndexImpl_TestCase.java │ │ ├── AnnotationPropertyRangeAxiomsIndexImpl_TestCase.java │ │ ├── AxiomChangeHandler_TestCase.java │ │ ├── AxiomMultimapIndex_UnaryKey_TestCase.java │ │ ├── AxiomMultimap_Nary_TestCase.java │ │ ├── AxiomsByEntityReferenceIndexImpl_ContainsEntityInOntologyAxiomsSignature_TestCase.java │ │ ├── AxiomsByEntityReferenceIndexImpl_TestCase.java │ │ ├── AxiomsByReferenceIndexImpl_TestCase.java │ │ ├── AxiomsByTypeIndexImpl_TestCase.java │ │ ├── ClassAssertionAxiomsByClassIndexImpl_TestCase.java │ │ ├── ClassAssertionAxiomsByIndividualIndexImpl_TestCase.java │ │ ├── DataPropertyAssertionAxiomsBySubjectIndexImpl_TestCase.java │ │ ├── DataPropertyCharacteristicsIndexImpl_TestCase.java │ │ ├── DataPropertyDomainAxiomsIndexImpl_TestCase.java │ │ ├── DataPropertyRangeAxiomsIndex_TestCase.java │ │ ├── DeprecatedEntitiesByEntityIndexImpl_TestCase.java │ │ ├── DifferentIndividualsAxiomsIndexImpl_TestCase.java │ │ ├── DisjointClassesAxiomsIndexImpl_TestCase.java │ │ ├── DisjointDataPropertiesAxiomsIndexImpl_TestCase.java │ │ ├── DisjointObjectPropertiesAxiomsIndexImpl_TestCase.java │ │ ├── EntitiesInOntologySignatureByIriIndexImpl_TestCase.java │ │ ├── EntitiesInOntologySignatureIndexImpl_TestCase.java │ │ ├── EntitiesInProjectSignatureByIriIndexImpl_TestCase.java │ │ ├── EntitiesInProjectSignatureIndexImpl_TestCase.java │ │ ├── EquivalentClassesAxiomsIndexImpl_TestCase.java │ │ ├── EquivalentDataPropertiesAxiomsIndexImpl_TestCase.java │ │ ├── EquivalentObjectPropertiesAxiomsIndexImpl_TestCase.java │ │ ├── IndividualsByTypeIndexImpl_TestCase.java │ │ ├── InverseObjectPropertyAxiomsIndexImpl_TestCase.java │ │ ├── ObjectPropertyAssertionAxiomsBySubjectIndexImpl_TestCase.java │ │ ├── ObjectPropertyCharacteristicsIndexImpl_TestCase.java │ │ ├── ObjectPropertyDomainAxiomsIndexImpl_TestCase.java │ │ ├── ObjectPropertyRangeAxiomsIndexImpl_TestCase.java │ │ ├── OntologyAnnotationsIndexImpl_TestCase.java │ │ ├── OntologyAxiomsIndexImpl_TestCase.java │ │ ├── OntologySignatureByTypeIndexImpl_TestCase.java │ │ ├── OntologySignatureIndexImpl_TestCase.java │ │ ├── ProjectClassAssertionAxiomsByIndividualIndexImpl_TestCase.java │ │ ├── ProjectOntologiesIndexImpl_TestCase.java │ │ ├── ProjectSignatureByTypeIndexImpl_TestCase.java │ │ ├── ProjectSignatureIndexImpl_TestCase.java │ │ ├── PropertyAssertionAxiomsBySubjectIndexImpl_TestCase.java │ │ ├── RootIndexImpl_TestCase.java │ │ ├── SameIndividualAxiomsIndexImpl_TestCase.java │ │ ├── SubAnnotationPropertyAxiomsBySubPropertyIndexImpl_TestCase.java │ │ ├── SubAnnotationPropertyAxiomsBySuperPropertyIndexImpl_TestCase.java │ │ ├── SubClassOfAxiomsBySubClassIndexImpl_TestCase.java │ │ ├── SubDataPropertyAxiomsBySubPropertyIndexImpl_TestCase.java │ │ └── SubObjectPropertyAxiomsBySubPropertyIndexImpl_TestCase.java │ ├── inject │ └── ApplicationExecutorsRegistry_TestCase.java │ ├── issues │ ├── CommentNotificationEmailGenerator_TestCase.java │ ├── CommentParticipantsExtractor_TestCase.java │ ├── CommentRenderer_TestCase.java │ ├── DiscussionThreadParticipantsExtractor_TestCase.java │ ├── EntityDiscussionThreadRepository_IT.java │ └── events │ │ └── MentionParser_TestCase.java │ ├── lang │ ├── ActiveLanguagesManagerImpl_TestCase.java │ ├── DefaultDisplayNameSettingsFactory_TestCase.java │ └── LanguageCode_TestCase.java │ ├── mail │ ├── CommentMessageIdGenerator_TestCase.java │ ├── MessageIdGenerator_TestCase.java │ ├── MessageId_TestCase.java │ └── SendMailImplTestCase.java │ ├── manager │ └── WebProtegeOntologyManagerSaveBinaryDocumentTestCase.java │ ├── mansyntax │ ├── ManchesterSyntaxFrameParser_TestCase.java │ ├── OntologyAxiomPairChangeGeneratorTestCase.java │ ├── OntologyAxiomPairOntologySwitchTestCase.java │ ├── ShellOntologyChecker_TestCase.java │ └── ShellOwlOntology_TestCase.java │ ├── match │ ├── AndMatcher_TestCase.java │ ├── AnnotationMatcher_TestCase.java │ ├── AnnotationPropertyMatcher_TestCase.java │ ├── AnnotationValuesAreNotDisjointMatcher_TestCase.java │ ├── ConflictingBooleanValuesMatcher_TestCase.java │ ├── DateIsAfterMatcher_TestCase.java │ ├── DateIsBeforeMatcher_TestCase.java │ ├── EntityIsDeprecatedMatcher_TestCase.java │ ├── HierarchyPositionMatchingEngineImpl_TestCase.java │ ├── IriAnnotationValueMatcher_TestCase.java │ ├── IriLexicalValueMatcher_TestCase.java │ ├── LangTagMatchesMatcher_TestCase.java │ ├── LexicalValueNotInDatatypeSpaceMatcher_TestCase.java │ ├── LiteralAnnotationValueMatcher_TestCase.java │ ├── LiteralInLexicalSpaceMatcher_TestCase.java │ ├── LiteralMatcher_TestCase.java │ ├── NonUniqueLangTagsMatcher_TestCase.java │ ├── NotMatcher_TestCase.java │ ├── NumericValueMatcher_TestCase.java │ ├── OrMatcher_TestCase.java │ ├── StringContainsMatcher_TestCase.java │ ├── StringContainsRegexMatchMatcher_TestCase.java │ ├── StringContainsRepeatedWhiteSpaceMatcher_TestCase.java │ ├── StringEndsWithMatcher_TestCase.java │ ├── StringEqualsMatcher_TestCase.java │ └── StringStartsWithMatcher_TestCase.java │ ├── merge │ ├── AnnotationDiffCalculator_TestCase.java │ ├── AxiomDiffCalculator_TestCase.java │ ├── ModifiedProjectOntologiesCalculator_TestCase.java │ ├── OntologyDiff2Changes_TestCase.java │ ├── OntologyDiffCalculator_TestCase.java │ ├── OntologyDiff_TestCase.java │ ├── OntologyPatcher_TestCase.java │ └── ProjectOntologiesBuilder_TestCase.java │ ├── merge_add │ └── MergeOntologyCalculator_TestCase.java │ ├── metaproject │ └── UserDetailsManagerImpl_TestCase.java │ ├── object │ ├── OWLClassExpressionSelector_TestCase.java │ ├── OWLDataPropertyExpressionSelector_TestCase.java │ ├── OWLIndividualSelector_TestCase.java │ ├── OWLObjectPropertyExpressionSelector_TestCase.java │ └── SWRLAtomSelector_TestCase.java │ ├── ontology │ ├── ProcessUploadedOntologiesRequestTest.java │ └── ProcessUploadedOntologiesResponseTest.java │ ├── owlapi │ ├── LoadOBOOntologyDocument_TestCase.java │ ├── ProjectAnnotationAssertionAxiomsBySubjectIndexImpl_TestCase.java │ └── change │ │ └── RevisionManagerImpl_TestCase.java │ ├── permissions │ └── GetProjectPermissionsActionHandler_TestCase.java │ ├── persistence │ ├── EmailAddressReadConverterTestCase.java │ ├── EmailAddressWriteConverterTestCase.java │ ├── MilestoneReadConverter_TestCase.java │ ├── MilestoneWriteConverter_TestCase.java │ ├── OWLEntityReadConverter_TestCase.java │ ├── OWLEntityWriteConverter_TestCase.java │ ├── ProjectIdReadConverterTestCase.java │ ├── ProjectIdWriteConverterTestCase.java │ ├── UserIdReadConverterTestCase.java │ └── UserIdWriteConverterTestCase.java │ ├── perspective │ └── BuiltInPerspective_TestCase.java │ ├── place │ ├── PlaceUrl_TestCase.java │ ├── ProjectViewPlaceTokenizer_TestCase.java │ └── ProjectViewPlace_TestCase.java │ ├── project │ ├── BuiltInPrefixDeclarationsLoader_TestCase.java │ ├── CreateProjectSagaManagerTest.java │ ├── DefaultOntologyIdManagerImpl_TestCase.java │ ├── FileDocumentSourceMatcher.java │ ├── GetProjectDetailsActionHandler_TestCase.java │ ├── PrefixDeclarationsCsvParser_TestCase.java │ ├── PrefixDeclarationsStore_IT.java │ ├── ProjectAccessManagerImpl_IT.java │ ├── ProjectCache_Test.java │ ├── ProjectDetailsRepository_IT.java │ ├── RecentProjectRecord_TestCase.java │ ├── WebProtegeProjectComponent_TestCase.java │ └── chg │ │ ├── OntologyChangeTranslatorVisitor_TestCase.java │ │ └── OntologyChangeTranslator_TestCase.java │ ├── projectsettings │ └── GetProjectSettingsActionHandler_TestCase.java │ ├── renderer │ ├── AnnotationPropertyComparatorImpl_TestCase.java │ ├── IRIOrdinalProvider_TestCase.java │ ├── ImageLinkRendererTestCase.java │ ├── MarkdownLiteralRendererTestCase.java │ ├── NullDeprecatedEntityChecker_TestCase.java │ └── NullHighlightedEntityChecker_TestCase.java │ ├── revision │ ├── CreateInitialRevisionHistoryRequestTest.java │ ├── CreateInitialRevisionHistoryResponseTest.java │ ├── GetHeadRevisionNumberActionHandler_TestCase.java │ ├── GetRevisionSummariesActionHandler_TestCase.java │ └── ProjectChangesManager_IT.java │ ├── search │ └── EntitySearchFilterRepositoryImpl_IT.java │ ├── shortform │ ├── IndexingAnalyzerWrapper_TestCase.java │ ├── LocalNameExtractor_TestCase.java │ ├── ProjectLuceneDirectoryPathSupplier_TestCase.java │ ├── QueryAnalyzerFactory_TestCase.java │ └── WebProtegeOntologyIRIShortFormProvider_TestCase.java │ ├── tag │ ├── EntityTagsRepositoryImpl_TestCase.java │ └── TagRepositoryImpl_IT.java │ ├── trigger │ └── TriggerRunner_TestCase.java │ ├── ui │ ├── DisplayContextTest.java │ ├── ViewIdTest.java │ └── ViewNodeIdTest.java │ ├── user │ ├── GetUserIdCompletionsActionHandler_TestCase.java │ ├── GetUserIdCompletionsAction_TestCase.java │ ├── GetUserIdCompletionsResult_TestCase.java │ ├── UserActivityManager_IT.java │ ├── UserActivityRecord_TestCase.java │ ├── UserIdInitialsExtractor_TestCase.java │ └── UserRecord_TestCase.java │ ├── util │ ├── AlphaNumericStringComparator_TestCase.java │ ├── EntityDeleter_TestCase.java │ ├── OWLOntologyChangeDataVisitorAdapter_TestCase.java │ ├── ReferenceFinder_TestCase.java │ ├── TempFileFactoryImpl_TestCase.java │ └── UUIDUtil_TestCase.java │ ├── viz │ ├── EntityGraphBuilder_TestCase.java │ └── EntityGraphSettingsRepositoryImpl_IT.java │ ├── watches │ └── WatchRecordRepository_IT.java │ └── webhook │ ├── SlackWebhookRepository_IT.java │ └── WebhookRepositoryImpl_IT.java └── resources ├── application-integrationtest.properties ├── application-test.yaml ├── application.properties ├── edu └── stanford │ └── protege │ └── webprotege │ └── app │ └── UserInSession.json ├── ontologies └── obo │ └── go.fragment.obo └── orderedSiblingsTest.json /.github/workflows/ci.yaml: 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