@jbrowse/core 2.2.1 → 2.2.2

package/ui/AboutDialog.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { AnyConfigurationModel } from '../configuration';
-export declare function FileInfo({ config }: {
+export declare function FileInfoPanel({ config }: {
     config: AnyConfigurationModel;
 }): JSX.Element | null;
 export declare function AboutContents({ config }: {

package/ui/AboutDialog.js

@@ -26,29 +26,23 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.AboutContents = exports.FileInfo = void 0;
+exports.AboutContents = exports.FileInfoPanel = void 0;
 const react_1 = __importStar(require("react"));
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const material_1 = require("@mui/material");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 const mui_1 = require("tss-react/mui");
 const configuration_1 = require("../configuration");
+const Dialog_1 = __importDefault(require("./Dialog"));
 const LoadingEllipses_1 = __importDefault(require("./LoadingEllipses"));
 const util_1 = require("../util");
 const tracks_1 = require("../util/tracks");
 const BaseFeatureDetail_1 = require("../BaseFeatureWidget/BaseFeatureDetail");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
+const useStyles = (0, mui_1.makeStyles)()({
     content: {
         minWidth: 800,
     },
-}));
-function FileInfo({ config }) {
+});
+function FileInfoPanel({ config }) {
     const [error, setError] = (0, react_1.useState)();
     const [info, setInfo] = (0, react_1.useState)();
     const session = (0, util_1.getSession)(config);
@@ -89,7 +83,7 @@ function FileInfo({ config }) {
         : info || {};
     return info !== null ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "File info" }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : info === undefined ? (react_1.default.createElement(LoadingEllipses_1.default, { message: "Loading file data" })) : (react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: details })))) : null;
 }
-exports.FileInfo = FileInfo;
+exports.FileInfoPanel = FileInfoPanel;
 function AboutContents({ config }) {
     const [copied, setCopied] = (0, react_1.useState)(false);
     const conf = (0, configuration_1.readConfObject)(config);
@@ -115,7 +109,7 @@ function AboutContents({ config }) {
             react_1.default.createElement(BaseFeatureDetail_1.Attributes, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
         ExtraPanel ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: ExtraPanel.name },
             react_1.default.createElement(ExtraPanel.Component, { config: config }))) : null,
-        react_1.default.createElement(FileInfo, { config: config })));
+        react_1.default.createElement(FileInfoPanel, { config: config })));
 }
 exports.AboutContents = AboutContents;
 function AboutDialog({ config, handleClose, }) {
@@ -124,11 +118,7 @@ function AboutDialog({ config, handleClose, }) {
     const trackName = (0, tracks_1.getTrackName)(config, session);
     const { pluginManager } = (0, util_1.getEnv)(session);
     const AboutComponent = pluginManager.evaluateExtensionPoint('Core-replaceAbout', AboutContents, { session, config });
-    return (react_1.default.createElement(material_1.Dialog, { open: true, onClose: handleClose, maxWidth: "xl" },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            trackName,
-            react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose(), size: "large" },
-                react_1.default.createElement(Close_1.default, null))),
+    return (react_1.default.createElement(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.content },
             react_1.default.createElement(AboutComponent, { config: config }))));
 }

package/ui/Dialog.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { DialogProps } from '@mui/material';
+declare function JBrowseDialog(props: DialogProps & {
+    title: string;
+}): JSX.Element;
+declare const _default: typeof JBrowseDialog;
+export default _default;

package/ui/Dialog.js

@@ -0,0 +1,35 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+// icons
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+}));
+function JBrowseDialog(props) {
+    const { classes } = useStyles();
+    const { title, children, onClose } = props;
+    return (react_1.default.createElement(material_1.Dialog, { ...props },
+        react_1.default.createElement(material_1.ScopedCssBaseline, null,
+            react_1.default.createElement(material_1.DialogTitle, null,
+                title,
+                onClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => {
+                        // @ts-ignore
+                        onClose();
+                    } },
+                    react_1.default.createElement(Close_1.default, null))) : null),
+            react_1.default.createElement(material_1.Divider, null),
+            children)));
+}
+exports.default = (0, mobx_react_1.observer)(JBrowseDialog);

package/ui/FactoryResetDialog.js

@@ -3,13 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const Button_1 = __importDefault(require("@mui/material/Button"));
-const Dialog_1 = __importDefault(require("@mui/material/Dialog"));
-const DialogTitle_1 = __importDefault(require("@mui/material/DialogTitle"));
-const DialogContent_1 = __importDefault(require("@mui/material/DialogContent"));
-const DialogContentText_1 = __importDefault(require("@mui/material/DialogContentText"));
-const DialogActions_1 = __importDefault(require("@mui/material/DialogActions"));
 const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
 exports.default = ({ onClose, open, onFactoryReset, }) => {
     function handleDialogClose(action) {
         if (action === 'reset') {
@@ -17,11 +13,10 @@ exports.default = ({ onClose, open, onFactoryReset, }) => {
         }
         onClose();
     }
-    return (react_1.default.createElement(Dialog_1.default, { open: open, onClose: () => handleDialogClose() },
-        react_1.default.createElement(DialogTitle_1.default, { id: "alert-dialog-title" }, "Reset"),
-        react_1.default.createElement(DialogContent_1.default, null,
-            react_1.default.createElement(DialogContentText_1.default, { id: "alert-dialog-description" }, "Are you sure you want to reset? This will restore the default configuration.")),
-        react_1.default.createElement(DialogActions_1.default, null,
-            react_1.default.createElement(Button_1.default, { onClick: () => handleDialogClose(), color: "primary" }, "Cancel"),
-            react_1.default.createElement(Button_1.default, { onClick: () => handleDialogClose('reset'), color: "primary", variant: "contained" }, "OK"))));
+    return (react_1.default.createElement(Dialog_1.default, { title: "Reset", onClose: () => handleDialogClose(), open: open },
+        react_1.default.createElement(material_1.DialogContent, null,
+            react_1.default.createElement(material_1.DialogContentText, null, "Are you sure you want to reset? This will restore the default configuration.")),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { onClick: () => handleDialogClose(), color: "primary" }, "Cancel"),
+            react_1.default.createElement(material_1.Button, { onClick: () => handleDialogClose('reset'), color: "primary", variant: "contained" }, "OK"))));
 };

package/ui/ReturnToImportFormDialog.js

@@ -6,24 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    closeButton: {
-        position: 'absolute',
-        right: theme.spacing(1),
-        top: theme.spacing(1),
-        color: theme.palette.grey[500],
-    },
-}));
+const Dialog_1 = __importDefault(require("./Dialog"));
 function ReturnToImportFormDialog({ model, handleClose, }) {
-    const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose },
-        react_1.default.createElement(material_1.DialogTitle, null,
-            "Reference sequence",
-            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose(), size: "large" },
-                react_1.default.createElement(Close_1.default, null))) : null),
-        react_1.default.createElement(material_1.Divider, null),
+    return (react_1.default.createElement(Dialog_1.default, { maxWidth: "xl", open: true, onClose: handleClose, title: "Reference sequence" },
         react_1.default.createElement(material_1.DialogContent, null,
             react_1.default.createElement(material_1.Typography, null, "Are you sure you want to return to the import form? This will lose your current view")),
         react_1.default.createElement(material_1.DialogActions, null,

package/ui/index.d.ts

@@ -1,5 +1,6 @@
 export * from './theme';
 export { LogoFull, Logomark } from './Logo';
+export { default as Dialog } from './Dialog';
 export { default as App } from './App';
 export { default as ReturnToImportFormDialog } from './ReturnToImportFormDialog';
 export { default as ErrorMessage } from './ErrorMessage';

package/ui/index.js

@@ -17,11 +17,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.LoadingEllipses = exports.SanitizedHTML = exports.CascadingMenu = exports.Menu = exports.FatalErrorDialog = exports.Tooltip = exports.FactoryResetDialog = exports.EditableTypography = exports.ResizeHandle = exports.PrerenderedCanvas = exports.FileSelector = exports.AssemblySelector = exports.ErrorMessage = exports.ReturnToImportFormDialog = exports.App = exports.Logomark = exports.LogoFull = void 0;
+exports.LoadingEllipses = exports.SanitizedHTML = exports.CascadingMenu = exports.Menu = exports.FatalErrorDialog = exports.Tooltip = exports.FactoryResetDialog = exports.EditableTypography = exports.ResizeHandle = exports.PrerenderedCanvas = exports.FileSelector = exports.AssemblySelector = exports.ErrorMessage = exports.ReturnToImportFormDialog = exports.App = exports.Dialog = exports.Logomark = exports.LogoFull = void 0;
 __exportStar(require("./theme"), exports);
 var Logo_1 = require("./Logo");
 Object.defineProperty(exports, "LogoFull", { enumerable: true, get: function () { return Logo_1.LogoFull; } });
 Object.defineProperty(exports, "Logomark", { enumerable: true, get: function () { return Logo_1.Logomark; } });
+var Dialog_1 = require("./Dialog");
+Object.defineProperty(exports, "Dialog", { enumerable: true, get: function () { return __importDefault(Dialog_1).default; } });
 var App_1 = require("./App");
 Object.defineProperty(exports, "App", { enumerable: true, get: function () { return __importDefault(App_1).default; } });
 var ReturnToImportFormDialog_1 = require("./ReturnToImportFormDialog");

package/util/analytics.js

@@ -89,7 +89,10 @@ exports.writeGAAnalytics = writeGAAnalytics;
 function doAnalytics(rootModel, initialTimestamp, initialSessionQuery) {
     if (rootModel &&
         !(0, configuration_1.readConfObject)(rootModel.jbrowse.configuration, 'disableAnalytics')) {
+        // ok if these are unhandled
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery);
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         writeGAAnalytics(rootModel, initialTimestamp);
     }
 }

package/util/formatFastaStrings.d.ts

@@ -7,7 +7,7 @@ export interface SeqChunk {
  * ref https://stackoverflow.com/a/51506718/2129219
  *
  * @param seqString -  string
- * @returns formated sequence string
+ * @returns formatted sequence string
  */
 export declare function formatFastaLines(seqString: string): string;
 /**

package/util/formatFastaStrings.js

@@ -6,7 +6,7 @@ exports.formatSeqFasta = exports.formatFastaLines = void 0;
  * ref https://stackoverflow.com/a/51506718/2129219
  *
  * @param seqString -  string
- * @returns formated sequence string
+ * @returns formatted sequence string
  */
 function formatFastaLines(seqString) {
     return seqString.replace(/(.{1,80})/g, '$1\n').trimEnd();

package/util/index.d.ts

@@ -340,3 +340,4 @@ export declare function measureGridWidth(elements: string[]): number;
 export declare function getEnv(obj: any): {
     pluginManager: PluginManager;
 };
+export declare function dedupe<T, U>(results: T[] | undefined, cb: (result: T) => U): T[];

package/util/index.js

@@ -30,7 +30,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.bytesForRegions = exports.objectHash = exports.hashCode = exports.updateStatus = exports.generateCodonTable = exports.defaultCodonTable = exports.defaultStops = exports.defaultStarts = exports.measureText = exports.rIC = exports.blobToDataURL = exports.complement = exports.reverse = exports.revcom = exports.isElectron = exports.stringify = exports.shorten = exports.minmax = exports.renameRegionsIfNeeded = exports.renameRegionIfNeeded = exports.makeAbortableReaction = exports.findLastIndex = exports.iterMap = exports.bpSpanPx = exports.featureSpanPx = exports.cartesianToPolar = exports.polarToCartesian = exports.degToRad = exports.radToDeg = exports.bpToPx = exports.clamp = exports.compareLocStrings = exports.compareLocs = exports.parseLocString = exports.parseLocStringOneBased = exports.assembleLocStringFast = exports.assembleLocString = exports.getContainingDisplay = exports.getContainingTrack = exports.getContainingView = exports.getSession = exports.findParentThatIs = exports.springAnimate = exports.findParentThat = exports.useDebouncedCallback = exports.useDebounce = exports.inProduction = exports.inDevelopment = exports.isFeature = exports.SimpleFeature = void 0;
-exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
+exports.dedupe = exports.getEnv = exports.measureGridWidth = exports.getStr = exports.getUriLink = exports.useLocalStorage = exports.getLayoutId = exports.getViewParams = exports.getTickDisplayStr = exports.toLocale = exports.getBpDisplayStr = exports.supportedIndexingAdapters = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
 const react_1 = require("react");
 const is_object_1 = __importDefault(require("is-object"));
@@ -1010,3 +1010,7 @@ function getEnv(obj) {
     return (0, mobx_state_tree_1.getEnv)(obj);
 }
 exports.getEnv = getEnv;
+function dedupe(results = [], cb) {
+    return results.filter((elt, idx, self) => idx === self.findIndex(t => cb(t) === cb(elt)));
+}
+exports.dedupe = dedupe;

package/util/tracks.d.ts

@@ -31,7 +31,7 @@ export declare function storeBlobLocation(location: PreFileLocation): import("./
  * creates a new location from the provided location including the appropriate suffix and location type
  * @param location - the FileLocation
  * @param suffix - the file suffix (e.g. .bam)
- * @returns the constructed location object from the provided prameters
+ * @returns the constructed location object from the provided parameters
  */
 export declare function makeIndex(location: FileLocation, suffix: string): import("./types").BlobLocation | {
     uri: string;

package/util/tracks.js

@@ -87,7 +87,7 @@ exports.storeBlobLocation = storeBlobLocation;
  * creates a new location from the provided location including the appropriate suffix and location type
  * @param location - the FileLocation
  * @param suffix - the file suffix (e.g. .bam)
- * @returns the constructed location object from the provided prameters
+ * @returns the constructed location object from the provided parameters
  */
 function makeIndex(location, suffix) {
     if ('uri' in location) {