@jbrowse/product-core 5.0.0-beta.13 → 5.0.0-beta.14

package/esm/Session/Tracks.js

@@ -8,6 +8,9 @@ import { assertNotReaddedDifferently } from './readdedTrackConf.js';
 import { assertTrackConfOutlivesItsAssemblies } from './temporaryAssemblyTracks.js';
 /**
  * #stateModel TracksManagerSessionMixin
+ * Adds track configs to a session: looking one up by trackId among the
+ * config's tracks, assembly sequences and connection tracks, and adding or
+ * editing one.
  */
 export function TracksManagerSessionMixin(pluginManager) {
     return types

package/esm/Session/pluginExtraTrackItems.d.ts

@@ -1,11 +1,10 @@
-import type { SessionWithDialog } from './TrackMenu.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyTrackConfig } from '@jbrowse/core/configuration';
 import type { MenuItem } from '@jbrowse/core/ui';
-import type { TrackActionView } from '@jbrowse/core/util/types';
+import type { AbstractSessionModel, TrackActionView } from '@jbrowse/core/util/types';
 /**
  * plugin-contributed per-track items (`Core-extraTrackMenuItems`), surfaced in
  * both the hierarchical selector and the in-view label menu so plugins reach
  * every track menu consistently
  */
-export declare function pluginExtraTrackItems(pluginManager: PluginManager, session: SessionWithDialog, config: AnyTrackConfig, view?: TrackActionView): MenuItem[];
+export declare function pluginExtraTrackItems(pluginManager: PluginManager, session: AbstractSessionModel, config: AnyTrackConfig, view?: TrackActionView): MenuItem[];

package/esm/Session/pluginExtraTrackItems.js

@@ -6,7 +6,7 @@ import { buildExtraTrackMenuItems } from '@jbrowse/core/ui/buildExtraTrackMenuIt
  */
 export function pluginExtraTrackItems(pluginManager, session, config, view) {
     return buildExtraTrackMenuItems(pluginManager, {
-        session: session,
+        session,
         config,
         view,
     });

package/esm/sessionMigrations/index.js

@@ -40,14 +40,14 @@ function migrateDisplay(display, trackConfigId, resolve, collected) {
     if (typeof configuration !== 'string') {
         return { ...display, type: displayType.name };
     }
+    const meta = getConfigurationSchemaMetadata(displayType.configSchema);
     const lifted = {
         ...state?.lift(display),
-        ...(typeof display.heightPreConfig === 'number'
+        ...(typeof display.heightPreConfig === 'number' && meta?.definition.height
             ? { height: display.heightPreConfig }
             : {}),
     };
     const migrated = retired?.migrate?.(lifted) ?? lifted;
-    const meta = getConfigurationSchemaMetadata(displayType.configSchema);
     const settings = meta ? liftRetiredSpellings(meta, migrated) : migrated;
     const displayId = retired && configuration === `${trackConfigId}-${retired.type}`
         ? `${trackConfigId}-${displayType.name}`

package/esm/siblingCast.d.ts

@@ -1,5 +1,6 @@
 import type { BaseRootModel } from './RootModel/BaseRootModel.ts';
 import type { BaseSession } from './Session/BaseSession.ts';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
 /**
  * `types.compose` can't thread the types of sibling mixins into one another, so
  * a mixin that reaches members contributed by a co-composed base (`jbrowse`,
@@ -12,3 +13,8 @@ import type { BaseSession } from './Session/BaseSession.ts';
  */
 export declare function asSession<S>(self: S): S & BaseSession;
 export declare function asRoot<S>(self: S): S & BaseRootModel;
+/**
+ * A session mixin's `self` as the whole session, for handing to something
+ * declared over `AbstractSessionModel` (a dialog, a plugin extension point).
+ */
+export declare function asAbstractSession(self: unknown): AbstractSessionModel;

package/esm/siblingCast.js

@@ -14,3 +14,10 @@ export function asSession(self) {
 export function asRoot(self) {
     return self;
 }
+/**
+ * A session mixin's `self` as the whole session, for handing to something
+ * declared over `AbstractSessionModel` (a dialog, a plugin extension point).
+ */
+export function asAbstractSession(self) {
+    return self;
+}

package/esm/ui/AboutDialog.d.ts

@@ -1,6 +1,6 @@
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { AbstractSessionModel } from '@jbrowse/core/util';
-export default function AboutDialog({ config, session, handleClose, }: {
+declare const AboutDialog: ({ config, session, handleClose, }: {
     session: AbstractSessionModel;
     /**
      * the in-view track label passes `track.configuration`, a live node; the
@@ -9,4 +9,5 @@ export default function AboutDialog({ config, session, handleClose, }: {
      */
     config: AnyConfigurationModel | Record<string, unknown>;
     handleClose: () => void;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default AboutDialog;

package/esm/ui/AboutDialog.js

@@ -7,8 +7,9 @@ import Dialog from '@jbrowse/core/ui/Dialog';
 import { getEnv } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import { isStateTreeNode } from '@jbrowse/mobx-state-tree';
+import { observer } from 'mobx-react';
 import AboutContents from './AboutDialogContents.js';
-export default function AboutDialog({ config, session, handleClose, }) {
+const AboutDialog = observer(function AboutDialog({ config, session, handleClose, }) {
     const { pluginManager } = getEnv(session);
     // hydrated once here, so every panel and every plugin on the two About points
     // reads one live node: "Copy config" gives the same JSON whichever menu
@@ -17,4 +18,5 @@ export default function AboutDialog({ config, session, handleClose, }) {
         ? config
         : hydrateTrackConfig(pluginManager, config);
     return (_jsx(Dialog, { open: true, onClose: handleClose, title: getTrackName(config, session), maxWidth: "xl", children: live ? (_jsx(PluggableComponent, { pluginManager: pluginManager, name: "Core-replaceAbout", component: AboutContents, props: { config: live, session } })) : (_jsx(BaseCard, { title: "Configuration", children: _jsx(Attributes, { attributes: config }) })) }));
-}
+});
+export default AboutDialog;

package/esm/ui/DescriptionPanel.js

@@ -43,14 +43,14 @@ const useStyles = makeStyles()(theme => ({
         },
     },
 }));
-function Prose({ html }) {
+const Prose = observer(function Prose({ html }) {
     const { classes } = useStyles();
     return _jsx(SanitizedHTML, { html: html, className: classes.prose });
-}
-function DescriptionCard({ url, children, }) {
+});
+const DescriptionCard = observer(function DescriptionCard({ url, children, }) {
     const { classes } = useStyles();
     return (_jsxs(BaseCard, { title: "Description", children: [_jsxs(Typography, { variant: "caption", color: "textSecondary", component: "div", className: classes.provenance, children: ["The track's description, written for the UCSC Genome Browser \u2014 some display options it describes differ in JBrowse.", url ? (_jsxs(_Fragment, { children: [' ', _jsx(Link, { href: url, target: "_blank", rel: "noopener noreferrer", children: "View original" })] })) : null] }), children] }));
-}
+});
 const FetchedDescription = observer(function FetchedDescription({ url, }) {
     const { data: html, error, isLoading, } = useFetch(['trackDescriptionHtml', url], async (_name, url) => rebaseDescriptionHtml(await openLocation({ uri: url, locationType: 'UriLocation' }).readFile('utf8'), url));
     return (_jsx(DescriptionCard, { url: url, children: error ? (_jsx(ErrorBanner, { error: error })) : isLoading || html === undefined ? (_jsx(LoadingEllipses, { message: "Loading description" })) : (_jsx(Prose, { html: html })) }));

package/esm/ui/Drawer.js

@@ -6,38 +6,34 @@ import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
 const useStyles = makeStyles()(theme => ({
-    // The grid item, and the handle's containing block. Its own box rather than
-    // the Paper's because the Paper is the thing that SCROLLS: a handle
-    // positioned against it starts at the top of the scrolled content and rides
-    // away with it, and one taken out of flow with `position: fixed` is measured
-    // against the window instead — which is the same box only in a full-window
-    // app, and put a page-tall col-resize strip down an embedded view's page.
+    // The grid item. The handle is a flex sibling of the Paper, so it takes its
+    // own 4px instead of covering the widget's edge text.
     root: {
         // the drawer places itself, so a host renders it once wherever it likes
         // rather than on the side matching `drawerPosition` (see
         // `drawerGridTemplateColumns`)
         gridColumn: 'drawer',
-        position: 'relative',
+        // the last row: a drawer with no row of its own auto-places after the
+        // main item and drops to a new row when it sits on the left
+        gridRow: '-2 / -1',
+        display: 'flex',
         height: '100%',
         minWidth: 0,
     },
     paper: {
         overflowY: 'auto',
         height: '100%',
+        flex: 1,
+        minWidth: 0,
         // widgets position their own overlays against this
         position: 'relative',
         zIndex: DRAWER_Z_INDEX,
         outline: 'none',
         background: theme.palette.background.default,
     },
-    resizeHandle: {
-        position: 'absolute',
-        top: 0,
-        zIndex: DRAWER_Z_INDEX + 1,
-    },
-    // whichever edge faces the main content
-    handleForLeftDrawer: { right: 0 },
-    handleForRightDrawer: { left: 0 },
+    resizeHandle: { flexShrink: 0 },
+    handleForLeftDrawer: { order: 1 },
+    handleForRightDrawer: { order: -1 },
 }));
 /**
  * The drawer's chrome: the paper it sits on and the handle that resizes it.

package/esm/ui/HeaderButtons.d.ts

@@ -3,5 +3,5 @@ interface HeaderButtonsProps {
     hideUris?: boolean;
     setShowRefNames: (show: boolean) => void;
 }
-declare function HeaderButtons({ conf, hideUris, setShowRefNames, }: HeaderButtonsProps): import("react").JSX.Element;
+declare const HeaderButtons: ({ conf, hideUris, setShowRefNames, }: HeaderButtonsProps) => import("react").JSX.Element;
 export default HeaderButtons;

package/esm/ui/HeaderButtons.js

@@ -3,6 +3,7 @@ import { CopyToClipboardButton } from '@jbrowse/core/ui';
 import { stripBaseUris } from '@jbrowse/core/util/addRelativeUris';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Button } from '@mui/material';
+import { observer } from 'mobx-react';
 const useStyles = makeStyles()(theme => ({
     button: {
         float: 'right',
@@ -15,10 +16,10 @@ const useStyles = makeStyles()(theme => ({
         justifyContent: 'flex-end',
     },
 }));
-function HeaderButtons({ conf, hideUris, setShowRefNames, }) {
+const HeaderButtons = observer(function HeaderButtons({ conf, hideUris, setShowRefNames, }) {
     const { classes } = useStyles();
     return (_jsx("span", { className: classes.button, children: _jsxs("span", { className: classes.buttons, children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
                         setShowRefNames(true);
                     }, children: "Show ref names" }), hideUris ? null : (_jsx(CopyToClipboardButton, { variant: "contained", value: () => JSON.stringify(stripBaseUris(structuredClone(conf)), null, 2), children: "Copy config" }))] }) }));
-}
+});
 export default HeaderButtons;

package/esm/ui/PreferenceCheckbox.d.ts

@@ -1,6 +1,7 @@
-export default function PreferenceCheckbox({ checked, label, help, onChange, }: {
+declare const PreferenceCheckbox: ({ checked, label, help, onChange, }: {
     checked: boolean;
     label: string;
     help?: string;
     onChange: (checked: boolean) => void;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default PreferenceCheckbox;

package/esm/ui/PreferenceCheckbox.js

@@ -2,15 +2,17 @@ import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-run
 import { LabeledCheckbox } from '@jbrowse/core/ui';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
 const useStyles = makeStyles()({
     row: {
         alignItems: 'flex-start',
         marginTop: 8,
     },
 });
-export default function PreferenceCheckbox({ checked, label, help, onChange, }) {
+const PreferenceCheckbox = observer(function PreferenceCheckbox({ checked, label, help, onChange, }) {
     const { classes } = useStyles();
     return (_jsx(LabeledCheckbox, { className: classes.row, checked: checked, onChange: checked => {
             onChange(checked);
         }, label: _jsxs(_Fragment, { children: [_jsx(Typography, { children: label }), help ? (_jsx(Typography, { variant: "body2", color: "text.secondary", children: help })) : null] }) }));
-}
+});
+export default PreferenceCheckbox;

package/esm/ui/WidgetHeading.d.ts

@@ -1,7 +1,7 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { Widget } from '@jbrowse/core/util';
-declare function WidgetHeading({ widget, pluginManager, }: {
+declare const WidgetHeading: ({ widget, pluginManager, }: {
     widget: Widget;
     pluginManager: PluginManager;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
 export default WidgetHeading;

package/esm/ui/WidgetHeading.js

@@ -1,7 +1,8 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { Typography } from '@mui/material';
-function WidgetHeading({ widget, pluginManager, }) {
+import { observer } from 'mobx-react';
+const WidgetHeading = observer(function WidgetHeading({ widget, pluginManager, }) {
     const { HeadingComponent, heading } = pluginManager.getWidgetType(widget.type);
     return HeadingComponent ? (_jsx(HeadingComponent, { model: widget })) : (_jsx(Typography, { variant: "h6", color: "inherit", children: heading }));
-}
+});
 export default WidgetHeading;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "5.0.0-beta.13",
+  "version": "5.0.0-beta.14",
   "type": "module",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
@@ -28,13 +28,13 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.7.0",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
     "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
-    "@jbrowse/render-core": "^5.0.0-beta.13",
-    "@jbrowse/core": "^5.0.0-beta.13"
+    "@jbrowse/render-core": "^5.0.0-beta.14",
+    "@jbrowse/core": "^5.0.0-beta.14"
   },
   "peerDependencies": {
     "react": ">=19.0.0",