@gen-epix/ui 1.14.4 → 1.15.0

package/src/index.ts

@@ -0,0 +1,301 @@
+// This file is auto-generated by Vite. Do not edit manually.
+
+export * from './utils/ValidationUtil';
+export * from './utils/UserManagerUtil';
+export * from './utils/TimeUtil';
+export * from './utils/TestIdUtil';
+export * from './utils/TableUtil';
+export * from './utils/StringUtil';
+export * from './utils/QueryUtil';
+export * from './utils/OutageUtil';
+export * from './utils/ObjectUtil';
+export * from './utils/NumberUtil';
+export * from './utils/NotificationUtil';
+export * from './utils/NewickUtil';
+export * from './utils/MenuDataUtil';
+export * from './utils/FormUtil';
+export * from './utils/FileUtil';
+export * from './utils/EpiUploadUtil';
+export * from './utils/EpiTreeUtil';
+export * from './utils/EpiMapUtil';
+export * from './utils/EpiLineListUtil';
+export * from './utils/EpiFilterUtil';
+export * from './utils/EpiCurveUtil';
+export * from './utils/EffectiveRightsUtil';
+export * from './utils/DownloadUtil';
+export * from './utils/DataUtil';
+export * from './utils/DataSetUtil';
+export * from './utils/DataHookUtil';
+export * from './utils/DashboardUtil';
+export * from './utils/CaseUtil';
+export * from './utils/CaseTypeUtil';
+export * from './utils/CaseSetUtil';
+export * from './utils/CaseSelectionUtil';
+export * from './utils/AxiosUtil';
+export * from './utils/AbacUtil';
+export * from './stores/userProfileStore';
+export * from './stores/tableStore';
+export * from './stores/outagesStore';
+export * from './stores/oidcStore';
+export * from './stores/epiUploadStore';
+export * from './stores/epiDashboardStore';
+export * from './setup';
+export * from './routes';
+export * from './pages/UsersAdminPage';
+export * from './pages/UserShareCasePoliciesAdminPage';
+export * from './pages/UserInvitationsAdminPage';
+export * from './pages/UserEffectiveRightsTesterAdminPage';
+export * from './pages/UserEffectiveRightsAdminPage';
+export * from './pages/UserAccessCasePoliciesAdminPage';
+export * from './pages/UploadPage';
+export * from './pages/TrendsPage';
+export * from './pages/RouterErrorPage';
+export * from './pages/RegionsAdminPage';
+export * from './pages/RegionSetsAdminPage';
+export * from './pages/RegionSetShapesAdminPage';
+export * from './pages/RegionRelationsAdminPage';
+export * from './pages/RefDimsAdminPage';
+export * from './pages/RefColsAdminPage';
+export * from './pages/PostLogoutPage';
+export * from './pages/PostLoginPage';
+export * from './pages/OutagesAdminPage';
+export * from './pages/OrganizationsAdminPage';
+export * from './pages/OrganizationSitesAdminPage';
+export * from './pages/OrganizationShareCasePoliciesAdminPage';
+export * from './pages/OrganizationContactsAdminPage';
+export * from './pages/OrganizationAdminPoliciesAdminPage';
+export * from './pages/OrganizationAccessCasePoliciesAdminPage';
+export * from './pages/IdentifierIssuersAdminPage';
+export * from './pages/HomePage';
+export * from './pages/EventsPage';
+export * from './pages/EventsDetailPage';
+export * from './pages/EtiologiesAdminPage';
+export * from './pages/EtiologicalAgentsAdminPage';
+export * from './pages/ErrorPage';
+export * from './pages/DiseasesAdminPage';
+export * from './pages/DimsAdminPage';
+export * from './pages/DataCollectionsAdminPage';
+export * from './pages/DataCollectionVisualizationPage';
+export * from './pages/DataCollectionSetsAdminPage';
+export * from './pages/CrudPage';
+export * from './pages/ConceptsAdminPage';
+export * from './pages/ConceptSetsAdminPage';
+export * from './pages/ConceptRelationsAdminPage';
+export * from './pages/ColsAdminPage';
+export * from './pages/ColSetsAdminPage';
+export * from './pages/ChooseIdentityProviderPage';
+export * from './pages/CasesPage';
+export * from './pages/CasesDetailPage';
+export * from './pages/CaseTypesAdminPage';
+export * from './pages/CaseTypeSetsAdminPage';
+export * from './pages/CaseTypeSetCategoriesAdminPage';
+export * from './pages/CaseSetStatusAdminPage';
+export * from './pages/AdminPage';
+export * from './pages/AcceptInvitationPage';
+export * from './models/admin.ts';
+export * from './models/auth.ts';
+export * from './models/caseAccess.ts';
+export * from './models/config.ts';
+export * from './models/data.ts';
+export * from './models/dataHooks.ts';
+export * from './models/environment.ts';
+export * from './models/epi.ts';
+export * from './models/filter.ts';
+export * from './models/form.ts';
+export * from './models/generic.ts';
+export * from './models/nestedMenu.ts';
+export * from './models/notification.ts';
+export * from './models/outage.ts';
+export * from './models/query.ts';
+export * from './models/reactRouter.ts';
+export * from './models/table.ts';
+export * from './models/testId.ts';
+export * from './models/tree.ts';
+export * from './hooks/useUserCasePolicyNameFactory';
+export * from './hooks/useUpdateDocumentTitle';
+export * from './hooks/useUpdateBreadcrumb';
+export * from './hooks/useSubscribable';
+export * from './hooks/useScrollbarSize';
+export * from './hooks/useQueryMemo';
+export * from './hooks/useOrganizationCasePolicyNameFactory';
+export * from './hooks/useItemQuery';
+export * from './hooks/useIsFormFieldRequiredFromSchema';
+export * from './hooks/useInitializeTableStore';
+export * from './hooks/useEditMutation';
+export * from './hooks/useDimensions';
+export * from './hooks/useDeleteMutation';
+export * from './hooks/useCreateMutation';
+export * from './hooks/useColumnsMenu';
+export * from './hooks/useArray';
+export * from './hoc/withPermissions';
+export * from './hoc/withDialog';
+export * from './dataHooks/useUsersQuery';
+export * from './dataHooks/useUserShareCasePoliciesQuery';
+export * from './dataHooks/useUserEffectiveRightsQuery';
+export * from './dataHooks/useUserAccessCasePoliciesQuery';
+export * from './dataHooks/useTreeAlgorithmCodesQuery';
+export * from './dataHooks/useSequencingProtocolsQuery';
+export * from './dataHooks/useRegionSetsQuery';
+export * from './dataHooks/useRegionRelationTypeQuery';
+export * from './dataHooks/useRegionQuery';
+export * from './dataHooks/useRefDimsQuery';
+export * from './dataHooks/useRefColsValidationRulesQuery';
+export * from './dataHooks/useRefColsQuery';
+export * from './dataHooks/useOrganizationsQuery';
+export * from './dataHooks/useOrganizationShareCasePoliciesQuery';
+export * from './dataHooks/useOrganizationIdentifierIssuerLinksQuery';
+export * from './dataHooks/useOrganizationAdminPoliciesQuery';
+export * from './dataHooks/useOrganizationAccessCasePoliciesQuery';
+export * from './dataHooks/useInviteUserConstraintsQuery';
+export * from './dataHooks/useIdentifierIssuerQuery';
+export * from './dataHooks/useIdentifierIssuerOwnOrganizationQuery';
+export * from './dataHooks/useGeneticDistanceProtocolsQuery';
+export * from './dataHooks/useEtiologicalAgentsQuery';
+export * from './dataHooks/useDiseasesQuery';
+export * from './dataHooks/useDimsQuery';
+export * from './dataHooks/useDimTypesQuery';
+export * from './dataHooks/useDataCollectionsQuery';
+export * from './dataHooks/useDataCollectionSetMembersQuery';
+export * from './dataHooks/useConceptSetsQuery';
+export * from './dataHooks/useConceptSetTypeQuery';
+export * from './dataHooks/useConceptRelationTypeQuery';
+export * from './dataHooks/useConceptQuery';
+export * from './dataHooks/useColsQuery';
+export * from './dataHooks/useColTypesQuery';
+export * from './dataHooks/useColSetsQuery';
+export * from './dataHooks/useColSetMembersQuery';
+export * from './dataHooks/useCaseTypesQuery';
+export * from './dataHooks/useCaseTypeStatsQuery';
+export * from './dataHooks/useCaseTypeSetsQuery';
+export * from './dataHooks/useCaseTypeSetMembersQuery';
+export * from './dataHooks/useCaseTypeSetCategoriesQuery';
+export * from './dataHooks/useCaseSetsQuery';
+export * from './dataHooks/useCaseSetStatusesQuery';
+export * from './dataHooks/useCaseSetStatsQuery';
+export * from './dataHooks/useCaseSetRightsQuery';
+export * from './dataHooks/useCaseSetCategoriesQuery';
+export * from './dataHooks/useCaseRightsQuery';
+export * from './dataHooks/useAssemblyProtocolsQuery';
+export * from './data/date.ts';
+export * from './data/queryDependencies.ts';
+export * from './context/caseTypeAbac';
+export * from './context/caseAbac';
+export * from './components/ui/UsersEffectiveRightsDetailsDialog';
+export * from './components/ui/UserInactivityConfirmation';
+export * from './components/ui/UserFeedbackDialog';
+export * from './components/ui/Table';
+export * from './components/ui/Stepper';
+export * from './components/ui/Spinner';
+export * from './components/ui/Sidebar';
+export * from './components/ui/ResponseHandler';
+export * from './components/ui/PanelSeparator';
+export * from './components/ui/PageContainer';
+export * from './components/ui/OutagesDialog';
+export * from './components/ui/OutageList';
+export * from './components/ui/OrganizationSwitcherDialog';
+export * from './components/ui/Notifications';
+export * from './components/ui/NestedMenu';
+export * from './components/ui/NavLink';
+export * from './components/ui/MyPermissionsDialog';
+export * from './components/ui/LoadingIndicator';
+export * from './components/ui/LinearProgressWithLabel';
+export * from './components/ui/LicensesDialog';
+export * from './components/ui/HomePageTrends';
+export * from './components/ui/GenericErrorMessage';
+export * from './components/ui/FileSelector';
+export * from './components/ui/Dialog';
+export * from './components/ui/CopyToClipboardButton';
+export * from './components/ui/ConsentDialog';
+export * from './components/ui/Confirmation';
+export * from './components/ui/Breadcrumbs';
+export * from './components/ui/AuthorizationWrapper';
+export * from './components/ui/AuthenticationWrapper';
+export * from './components/ui/ApplicationFooter';
+export * from './components/ui/ApplicationBar';
+export * from './components/form/helpers/GenericForm';
+export * from './components/form/helpers/FormFieldLoadingIndicator';
+export * from './components/form/helpers/FormFieldHelperText';
+export * from './components/form/fields/TransferList';
+export * from './components/form/fields/ToggleButtonGroup';
+export * from './components/form/fields/TextField';
+export * from './components/form/fields/Switch';
+export * from './components/form/fields/Select';
+export * from './components/form/fields/RichTextEditor';
+export * from './components/form/fields/RadioGroup';
+export * from './components/form/fields/NumberRangeInput';
+export * from './components/form/fields/NumberField';
+export * from './components/form/fields/DateRangePicker';
+export * from './components/form/fields/DatePicker';
+export * from './components/form/fields/CheckboxGroup';
+export * from './components/form/fields/Autocomplete';
+export * from './components/filters/TextFilterField';
+export * from './components/filters/NumberRangeFilterField';
+export * from './components/filters/MultiSelectFilterField';
+export * from './components/filters/GeoFilterField';
+export * from './components/filters/DateFilterField';
+export * from './components/filters/BooleanFilterField';
+export * from './components/epi/EpiWidgetUnavailable';
+export * from './components/epi/EpiWidgetMenu';
+export * from './components/epi/EpiWidgetHeaderIconButton';
+export * from './components/epi/EpiWidget';
+export * from './components/epi/EpiWarning';
+export * from './components/epi/EpiUserRightsDialog';
+export * from './components/epi/EpiUpload';
+export * from './components/epi/EpiTreeDescription';
+export * from './components/epi/EpiTree';
+export * from './components/epi/EpiStratification';
+export * from './components/epi/EpiSequenceDownloadDialog';
+export * from './components/epi/EpiRemoveCasesFromEventDialog';
+export * from './components/epi/EpiMap';
+export * from './components/epi/EpiLineList';
+export * from './components/epi/EpiLegendaItem';
+export * from './components/epi/EpiFindSimilarCasesDialog';
+export * from './components/epi/EpiDataCollectionAccessInfo';
+export * from './components/epi/EpiDashboardStoreLoader';
+export * from './components/epi/EpiDashboard';
+export * from './components/epi/EpiCustomTabPanel';
+export * from './components/epi/EpiCurve';
+export * from './components/epi/EpiCreateEventDialog';
+export * from './components/epi/EpiContextMenu';
+export * from './components/epi/EpiContactDetailsDialog';
+export * from './components/epi/EpiCompletCaseTypeLoader';
+export * from './components/epi/EpiCasesAlreadyInCaseSetWarning';
+export * from './components/epi/EpiCaseTypeInfoDialog';
+export * from './components/epi/EpiCaseSummary';
+export * from './components/epi/EpiCaseSetInfoDialog';
+export * from './components/epi/EpiCaseInfoDialog';
+export * from './components/epi/EpiBulkEditCaseDialog';
+export * from './components/epi/EpiAddCasesToEventDialog';
+export * from './components/app/RouterRoot';
+export * from './components/app/ApplicationBootstrap';
+export * from './components/app/App';
+export * from './classes/managers/WindowManager';
+export * from './classes/managers/UserSettingsManager';
+export * from './classes/managers/RouterManager';
+export * from './classes/managers/QueryClientManager';
+export * from './classes/managers/PageEventBusManager';
+export * from './classes/managers/NotificationManager';
+export * from './classes/managers/NavigationHistoryManager';
+export * from './classes/managers/LogManager';
+export * from './classes/managers/KeyboardShortcutManager';
+export * from './classes/managers/InactivityManager';
+export * from './classes/managers/I18nManager';
+export * from './classes/managers/FeatureFlagsManager';
+export * from './classes/managers/EpiLineListCaseSetMembersManager';
+export * from './classes/managers/EpiHighlightingManager';
+export * from './classes/managers/EpiEventBusManager';
+export * from './classes/managers/EpiDataManager';
+export * from './classes/managers/EmotionCacheManager';
+export * from './classes/managers/DevicePixelRatioManager';
+export * from './classes/managers/ConfigManager';
+export * from './classes/managers/BreadcrumbManager';
+export * from './classes/managers/BackendVersionManager';
+export * from './classes/managers/AuthorizationManager';
+export * from './classes/managers/AuthenticationManager';
+export * from './classes/errors';
+export * from './classes/abstracts/SubscribableAbstract';
+export * from './classes/abstracts/FilterAbstract';
+export * from './classes/abstracts/EventBusAbstract';
+export * from './classes/TableEventBus';
+export * from './classes/Subject';
+export * from './api';

package/src/models/admin.ts

@@ -0,0 +1,7 @@
+export enum ADMIN_PAGE_CATEGORY {
+  USERS_AND_ORGANIZATIONS = 'USERS_AND_ORGANIZATIONS',
+  ACCESS_RIGHTS = 'ACCESS_RIGHTS',
+  REFERENCE_DATA = 'REFERENCE_DATA',
+  SYSTEM = 'SYSTEM',
+  HELPERS = 'HELPERS',
+}

package/src/models/auth.ts

@@ -0,0 +1,14 @@
+import type { Path } from 'react-router-dom';
+
+import type { IdentityProvider } from '../api';
+
+export type AuthState = {
+  preLoginLocation: Path;
+  lastRedirectTimestamp?: number;
+  redirectCounter?: number;
+};
+
+export type IdentityProviderWithAvailability = {
+  provider: IdentityProvider;
+  isAvailable: boolean;
+};

package/src/models/caseAccess.ts

@@ -0,0 +1,21 @@
+import type {
+  OrganizationAccessCasePolicy,
+  UserAccessCasePolicy,
+  UserShareCasePolicy,
+} from '../api';
+
+export type UserEffectiveRightCaseTypes = {
+  readonly case_type_set_ids: string[];
+  readonly uncategorized_case_type_ids: string[];
+  readonly categorized_case_type_ids: string[];
+};
+
+export type UserEffectiveRight = Omit<OrganizationAccessCasePolicy & UserAccessCasePolicy, 'id' | 'user_id' | 'is_active' | 'case_type_set_id'> & UserEffectiveRightCaseTypes & {
+  readonly read_col_set_ids: string[];
+  readonly uncategorized_read_col_ids: string[];
+  readonly categorized_read_col_ids: string[];
+  readonly write_col_set_ids: string[];
+  readonly uncategorized_write_col_ids: string[];
+  readonly categorized_write_col_ids: string[];
+  readonly effective_share_case_rights: Array<UserEffectiveRightCaseTypes & Pick<UserShareCasePolicy, 'add_case' | 'remove_case' | 'add_case_set' | 'remove_case_set' | 'from_data_collection_id'>>;
+};

package/src/models/config.ts

@@ -0,0 +1,153 @@
+import type { ReactElement } from 'react';
+import type {
+  CircularProgressProps,
+  Theme,
+} from '@mui/material';
+import type { TFunction } from 'i18next';
+
+import type { ColType } from '../api';
+
+import type {
+  EPI_ZONE,
+  EpiDashboardLayoutConfig,
+} from './epi';
+
+export type ApplicationHeaderProps = {
+  readonly fullWidth?: boolean;
+  readonly fullHeight?: boolean;
+  readonly singleAction?: boolean;
+};
+
+export type FooterSectionItem = {
+  readonly label: string;
+  readonly href?: string;
+  readonly onClick?: () => void;
+};
+
+export type FooterSection = {
+  readonly header: string;
+  readonly items: FooterSectionItem[];
+};
+
+export type FooterConfig = {
+  sections: FooterSection[];
+};
+
+export type I18nConfig = {
+  bundles: string[];
+  code: string;
+};
+
+export interface Config {
+  i18n: {
+    getCurrentLanguageCode: () => Promise<string>;
+    setNewLanguageCode: (code: string) => Promise<void>;
+    languages: I18nConfig[];
+  };
+  enablePageEvents: boolean;
+  applicationName: string;
+  createFooter: (t: TFunction<'translation', undefined>) => FooterConfig;
+  nonce?: string;
+  theme: Theme;
+  // eslint-disable-next-line @typescript-eslint/naming-convention
+  ApplicationHeader: (props: ApplicationHeaderProps) => ReactElement;
+  // eslint-disable-next-line @typescript-eslint/naming-convention
+  HomePageIntroduction: () => ReactElement;
+  // eslint-disable-next-line @typescript-eslint/naming-convention
+  LicenseInformation: () => ReactElement;
+  getSoftwareVersion: () => string;
+  getAPIBaseUrl: () => string;
+  getTouchIconUrl: () => string;
+  defaultRequestTimeout: number;
+  getEnvironmentMessage: (t: TFunction<'translation', undefined>) => string;
+  consentDialog: {
+    // eslint-disable-next-line @typescript-eslint/naming-convention
+    Content: () => ReactElement;
+    getShouldShow: () => boolean;
+    getTitle: (t: TFunction<'translation', undefined>) => string;
+    getButtonLabel: (t: TFunction<'translation', undefined>) => string;
+  };
+  trends: {
+    homePage: {
+      getSinceLabel: (t: TFunction<'translation', undefined>) => string;
+      // yyyy-MM-dd
+      getSinceDate: () => string;
+    };
+  };
+  notifications: {
+    autoHideAfterMs: number;
+  };
+  epi: {
+    ALLOWED_COL_TYPES_FOR_STRATIFICATION: ColType[];
+    DATA_MISSING_CHARACTER: string;
+    STRATIFICATION_COLORS: string[];
+    STRATIFICATION_COLOR_ITEM_MISSING: string;
+    INITIAL_NUM_VISIBLE_ATTRIBUTES_IN_CASE_SUMMARY: number;
+    DOWNLOAD_SECTION_ORDER: EPI_ZONE[];
+    SEQDB_MAX_STORED_DISTANCE_FALLBACK: number;
+  };
+  epiMap: {
+    MIN_PIE_CHART_RADIUS: number;
+  };
+  epiTree: {
+    MIN_SCALE_WIDTH_PX: number;
+    MAX_SCALE_WIDTH_PX: number;
+    SCALE_INCREMENTS: number[];
+    LEAF_DOT_RADIUS: number;
+    ANCESTOR_DOT_RADIUS: number;
+    MINIMUM_DISTANCE_PERCENTAGE_TO_SHOW_LABEL: number;
+    REGULAR_FILL_COLOR_SUPPORT_LINE: string;
+    HEADER_HEIGHT: number;
+    TREE_PADDING: number;
+    LINKED_SCROLL_DEBOUNCE_DELAY_MS: number;
+    MAX_ZOOM_LEVEL: number;
+    MIN_ZOOM_LEVEL: number;
+    MIN_ZOOM_SPEED: number;
+    PANNING_THRESHOLD: number;
+    INITIAL_UNLINKED_ZOOM_LEVEL: number;
+    MAX_ZOOM_SPEED: number;
+    TAKING_LONGER_TIMEOUT_MS: number;
+  };
+  epiLineList: {
+    TABLE_ROW_HEIGHT: number;
+    MAX_COLUMN_WIDTH: number;
+    REQUIRED_EXTRA_CELL_PADDING_TO_FIT_CONTENT: number;
+    CASE_SET_MEMBERS_FETCH_DEBOUNCE_DELAY_MS: number;
+  };
+  epiDashboard: {
+    MIN_PANEL_WIDTH: number;
+    MIN_PANEL_HEIGHT: number;
+    LAYOUTS: EpiDashboardLayoutConfig[];
+  };
+  spinner: {
+    DEFAULT_TAKING_LONGER_TIMEOUT_MS: number;
+    DEFAULT_CIRCULAR_PROGRESS_SIZE: CircularProgressProps['size'];
+  };
+  layout: {
+    SIDEBAR_MENU_WIDTH: number;
+    MAIN_CONTENT_ID: string;
+  };
+  userFeedback: {
+    SHOW_USER_FEEDBACK_TOOLTIP_AFTER_MS: number;
+  };
+  log: {
+    LOG_INTERVAL_MS: number;
+  };
+  userInactivityConfirmation: {
+    ALLOWED_IDLE_TIME_MS: number;
+    NOTIFICATION_TIME_MS: number;
+  };
+  outages: {
+    NUM_HOURS_TO_SHOW_SOON_ACTIVE_OUTAGES: number;
+  };
+  table: {
+    DEFAULT_OVERSCAN_MAIN: number;
+    DEFAULT_OVERSCAN_REVERSE: number;
+  };
+  login?: {
+    // eslint-disable-next-line @typescript-eslint/naming-convention
+    AfterIdentityProviderSelection?: () => ReactElement;
+    // eslint-disable-next-line @typescript-eslint/naming-convention
+    AfterLoginElement?: () => ReactElement;
+  };
+}

package/src/models/data.ts

@@ -0,0 +1,11 @@
+export type ConvertType<T, K> = {
+  [P in keyof T]: K;
+};
+
+export type DeepPartial<T> = {
+  [P in keyof T]?: DeepPartial<T[P]>;
+};
+
+export interface GenericData {
+  id?: string;
+}

package/src/models/dataHooks.ts

@@ -0,0 +1,18 @@
+import type { OptionBase } from './form';
+
+export interface UseOptions<TValue> extends Loadable {
+  options: OptionBase<TValue>[];
+}
+
+export interface UseMap<TValue> extends Loadable {
+  map: Map<string, TValue>;
+}
+
+export interface UseNameFactory<TValue> extends Loadable {
+  getName: (item: TValue) => string;
+}
+
+export interface Loadable {
+  isLoading: boolean;
+  error: unknown;
+}

package/src/models/environment.ts

@@ -0,0 +1,10 @@
+export type EnvironmentSettings = {
+  VITE_RELEASED_VERSION: string;
+  API_BASE_URL: string;
+  ENVIRONMENT_MESSAGE: string;
+  BASE_URL: string;
+  MODE: string;
+  DEV: boolean;
+  PROD: boolean;
+  SSR: boolean;
+};