@jbrowse/product-core 5.0.0-beta.10 → 5.0.0-beta.11

package/esm/Session/DrawerWidgets.d.ts

@@ -86,6 +86,8 @@ export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager):
     showWidget(widget: any): void;
     /**
      * #action
+     * closes the widget, and removes it from the session when its type sets
+     * `discardOnClose`. Minimizing the drawer is not closing.
      */
     hideWidget(widget: any): void;
     /**

package/esm/Session/DrawerWidgets.js

@@ -1,6 +1,6 @@
 import { isConfigurationModel } from '@jbrowse/core/configuration';
-import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util';
-import { addDisposer, getEnv, isAlive, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
+import { localStorageGetItem, localStorageSetItem, scheduleDetachedDestroy, } from '@jbrowse/core/util';
+import { addDisposer, detach, getEnv, isAlive, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { isBaseSession } from './BaseSession.js';
 const minDrawerWidth = 128;
@@ -171,12 +171,19 @@ export function DrawerWidgetSessionMixin(pluginManager) {
         },
         /**
          * #action
+         * closes the widget, and removes it from the session when its type sets
+         * `discardOnClose`. Minimizing the drawer is not closing.
          */
         hideWidget(widget) {
             self.activeWidgets.delete(widget.id);
             if (self.activeWidgets.size === 0) {
                 self.poppedOut = false;
             }
+            if (self.widgets.get(widget.id) === widget &&
+                pluginManager.getWidgetType(widget.type).discardOnClose) {
+                detach(widget);
+                scheduleDetachedDestroy(widget);
+            }
         },
         /**
          * #action
@@ -213,7 +220,9 @@ export function DrawerWidgetSessionMixin(pluginManager) {
          * #action
          */
         hideAllWidgets() {
-            self.activeWidgets.clear();
+            for (const widget of [...self.activeWidgets.values()]) {
+                this.hideWidget(widget);
+            }
             self.poppedOut = false;
         },
         afterAttach() {

package/esm/Session/MultipleViews.js

@@ -162,11 +162,11 @@ export function MultipleViewsSessionMixin(pluginManager) {
                 viewIdsWithin(view).includes(focusedViewId)) {
                 self.setFocusedViewId(undefined);
             }
-            // Every widget, not the active ones: a widget the user closed keeps
-            // its references and its autoruns. One that pointed into the view is
-            // now empty, so hide it rather than leave the panel showing what it no
-            // longer has.
-            for (const [, widget] of self.widgets) {
+            // Every widget, not the active ones: a closed widget that stays in the
+            // session keeps its references and its autoruns. One that pointed into
+            // the view is now empty, so close it rather than leave the panel
+            // showing what it no longer has.
+            for (const widget of [...self.widgets.values()]) {
                 if (dropRefsInto(widget, view)) {
                     self.hideWidget(widget);
                 }

package/esm/controllerTracks.js

@@ -1,10 +1,10 @@
 import { getEnv } from '@jbrowse/core/util';
 import { withPageBaseUri } from '@jbrowse/core/util/addRelativeUris';
-import { guessTrackConf } from '@jbrowse/core/util/tracks';
+import { guessTrackConf, isLooseTrackConfig } from '@jbrowse/core/util/tracks';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { resolveLocalFileUris } from './localFiles.js';
 export function isLooseTrack(track) {
-    return typeof track === 'string' || (!('adapter' in track) && 'uri' in track);
+    return typeof track === 'string' || isLooseTrackConfig(track);
 }
 /**
  * Stamp the view's assembly onto a full-config track that omits

package/esm/ui/AboutDialogContents.js

@@ -12,6 +12,7 @@ import DescriptionPanel from './DescriptionPanel.js';
 import FileInfoPanel from './FileInfoPanel.js';
 import HeaderButtons from './HeaderButtons.js';
 import RefNameInfoDialog from './RefNameInfoDialog.js';
+import { omitTrackDescription } from './descriptionHtml.js';
 import { getAboutDialogConfig } from './util.js';
 const useStyles = makeStyles()({
     content: {
@@ -24,7 +25,7 @@ const AboutDialogContents = observer(function AboutDialogContents({ config, sess
     const [showRefNames, setShowRefNames] = useState(false);
     const { pluginManager } = getEnv(session);
     const { config: shown, hideUris } = getAboutDialogConfig({ config, session });
-    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: readConfObject(config), hideUris: hideUris, setShowRefNames: setShowRefNames }), _jsx(Attributes, { attributes: shown, omit: [...hideFields, 'metadata'], hideUris: hideUris })] }), shown.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: shown.metadata, hideUris: hideUris }) })) : null, _jsx(DescriptionPanel, { config: config, session: session }), _jsx(AssemblyInfoPanel, { config: config, session: session, hideUris: hideUris }), _jsx(PluggableComponents, { pluginManager: pluginManager, 
+    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [_jsx(HeaderButtons, { conf: readConfObject(config), hideUris: hideUris, setShowRefNames: setShowRefNames }), _jsx(Attributes, { attributes: shown, omit: [...hideFields, 'metadata'], hideUris: hideUris })] }), shown.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: omitTrackDescription(shown.metadata), hideUris: hideUris }) })) : null, _jsx(DescriptionPanel, { config: config, session: session }), _jsx(AssemblyInfoPanel, { config: config, session: session, hideUris: hideUris }), _jsx(PluggableComponents, { pluginManager: pluginManager, 
                 /** #extensionPoint Core-extraAboutPanel | sync | Add extra panels to a track's About dialog */
                 name: "Core-extraAboutPanel", props: { session, config } }), hideUris ? null : _jsx(FileInfoPanel, { config: config, session: session }), showRefNames ? (_jsx(RefNameInfoDialog, { session: session, config: config, onClose: () => {
                     setShowRefNames(false);

package/esm/ui/DescriptionPanel.js

@@ -1,4 +1,4 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Fragment as _Fragment, jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorBanner, LoadingEllipses, SanitizedHTML } from '@jbrowse/core/ui';
@@ -7,19 +7,56 @@ import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { useFetch } from '@jbrowse/core/util/useFetch';
 import { Link, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import { getDescriptionHtmlUrl, rebaseDescriptionHtml, } from './descriptionHtml.js';
+import { getTrackDescription, rebaseDescriptionHtml, } from './descriptionHtml.js';
 const useStyles = makeStyles()(theme => ({
     provenance: {
         marginBottom: theme.spacing(1),
     },
+    prose: {
+        display: 'block',
+        '& h1, & h2': {
+            fontSize: theme.typography.pxToRem(16),
+            fontWeight: theme.typography.fontWeightBold,
+            margin: theme.spacing(2, 0, 0.5),
+        },
+        '& h3, & h4': {
+            fontSize: theme.typography.pxToRem(14),
+            fontWeight: theme.typography.fontWeightBold,
+            margin: theme.spacing(1.5, 0, 0.5),
+        },
+        '& > :first-child': {
+            marginTop: 0,
+        },
+        '& p': {
+            margin: theme.spacing(0, 0, 1),
+        },
+        '& table': {
+            borderCollapse: 'collapse',
+            margin: theme.spacing(1, 0),
+        },
+        '& th, & td': {
+            padding: theme.spacing(0.25, 1),
+            border: `1px solid ${theme.palette.divider}`,
+        },
+        '& img': {
+            maxWidth: '100%',
+        },
+    },
 }));
-const DescriptionCard = observer(function DescriptionCard({ url, }) {
+function Prose({ html }) {
+    const { classes } = useStyles();
+    return _jsx(SanitizedHTML, { html: html, className: classes.prose });
+}
+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 (_jsxs(BaseCard, { title: "Description", children: [_jsxs(Typography, { variant: "caption", color: "textSecondary", component: "div", className: classes.provenance, children: ["From the track hub, written for the UCSC Genome Browser \u2014 some display options it describes differ in JBrowse.", ' ', _jsx(Link, { href: url, target: "_blank", rel: "noopener noreferrer", children: "View original" })] }), error ? (_jsx(ErrorBanner, { error: error })) : isLoading || html === undefined ? (_jsx(LoadingEllipses, { message: "Loading description" })) : (_jsx(SanitizedHTML, { html: html }))] }));
+    return (_jsx(DescriptionCard, { url: url, children: error ? (_jsx(ErrorBanner, { error: error })) : isLoading || html === undefined ? (_jsx(LoadingEllipses, { message: "Loading description" })) : (_jsx(Prose, { html: html })) }));
 });
 const DescriptionPanel = observer(function DescriptionPanel({ config, }) {
-    const url = getDescriptionHtmlUrl(readConfObject(config, 'metadata'));
-    return url ? _jsx(DescriptionCard, { url: url }) : null;
+    const description = getTrackDescription(readConfObject(config, 'metadata'));
+    return !description ? null : 'url' in description ? (_jsx(FetchedDescription, { url: description.url })) : (_jsx(DescriptionCard, { children: _jsx(Prose, { html: description.html }) }));
 });
 export default DescriptionPanel;

package/esm/ui/descriptionHtml.d.ts

@@ -1,20 +1,42 @@
+export type TrackDescription = {
+    url: string;
+} | {
+    html: string;
+};
 /**
- * The URL of a track's prose description page in its `metadata`, as a UCSC
- * track hub supplies it, and undefined for anything that is not an http(s) url
- * — the value reaches `openLocation` and an anchor's href, so a `javascript:`
- * or `file://` one does not become one here.
+ * A track's prose description in its `metadata`, as UCSC trackDb supplies it:
+ * a link to a page to fetch, or the page itself.
  *
  * Four spellings: `UCSCTrackHubConnection` spreads the trackDb stanza across
  * `metadata`, the bulk converter behind genomes.jbrowse.org nests it under
  * `metadata.ucsc` (~50,700 configs at permanent URLs), and the stanza key is
  * `html` for a track and `htmlPath` for an assembly. Both producers write an
- * escaped anchor rather than a bare url, so the href comes back through a parse
- * rather than a regex.
+ * escaped anchor for a hub's page, so the href comes back through a parse. The
+ * converter writes golden-path assemblies' pages inline, and only under `ucsc`
+ * is markup read as a page, so a track's own `html` column stays a column.
+ *
+ * A url is http(s) only: it reaches `openLocation` and an anchor's href.
+ * `path` names the key read, which the metadata card leaves out.
+ */
+export declare function findTrackDescription(metadata: unknown): {
+    description: {
+        url: string;
+        html?: undefined;
+    } | {
+        url?: undefined;
+        html: string;
+    };
+    path: string[];
+} | undefined;
+export declare function getTrackDescription(metadata: unknown): TrackDescription | undefined;
+/**
+ * `metadata` without the key its description came from, since the Description
+ * card shows that one.
  */
-export declare function getDescriptionHtmlUrl(metadata: unknown): string | undefined;
+export declare function omitTrackDescription(metadata: Record<string, unknown>): Record<string, unknown>;
 /**
- * A fetched description page as markup for `SanitizedHTML`: links and images
- * resolved against the page they came from rather than the JBrowse origin, and
+ * A description page as markup for `SanitizedHTML`: links and images resolved
+ * against the page they came from rather than the JBrowse origin, and
  * `<form>` dropped, which the sanitizer keeps and which in a document off a
  * third-party origin is a credential prompt wearing the app's own chrome.
  *

package/esm/ui/descriptionHtml.js

@@ -1,33 +1,86 @@
 function isRecord(value) {
     return typeof value === 'object' && value !== null;
 }
-function descriptionUrl(value) {
-    const href = new DOMParser()
-        .parseFromString(value, 'text/html')
-        .querySelector('a[href]')
-        ?.getAttribute('href');
-    const candidate = typeof href === 'string' ? href : value.trim();
-    return /^https?:\/\//i.test(candidate) ? candidate : undefined;
+function isHttpUrl(value) {
+    return /^https?:\/\//i.test(value);
 }
 /**
- * The URL of a track's prose description page in its `metadata`, as a UCSC
- * track hub supplies it, and undefined for anything that is not an http(s) url
- * — the value reaches `openLocation` and an anchor's href, so a `javascript:`
- * or `file://` one does not become one here.
+ * Where UCSC trackDb text sits when the golden-path assemblies the UCSC
+ * Genome Browser serves itself carry it inline: their `html` holds the page,
+ * written to render inside `hgTrackUi`, so its relative links (`hgTables`,
+ * `/goldenPath/help/…`) resolve against that.
+ */
+const UCSC_TRACK_PAGE = 'https://genome.ucsc.edu/cgi-bin/hgTrackUi';
+function parseDescription(value, inline) {
+    const body = new DOMParser().parseFromString(value, 'text/html').body;
+    const [first] = body.children;
+    if (!first) {
+        const text = value.trim();
+        return isHttpUrl(text) ? { url: text } : undefined;
+    }
+    const loneAnchor = body.children.length === 1 &&
+        first.matches('a[href]') &&
+        body.textContent.trim() === first.textContent.trim();
+    if (loneAnchor) {
+        const href = first.getAttribute('href') ?? '';
+        return isHttpUrl(href) ? { url: href } : undefined;
+    }
+    return inline
+        ? { html: rebaseDescriptionHtml(value, UCSC_TRACK_PAGE) }
+        : undefined;
+}
+/**
+ * A track's prose description in its `metadata`, as UCSC trackDb supplies it:
+ * a link to a page to fetch, or the page itself.
  *
  * Four spellings: `UCSCTrackHubConnection` spreads the trackDb stanza across
  * `metadata`, the bulk converter behind genomes.jbrowse.org nests it under
  * `metadata.ucsc` (~50,700 configs at permanent URLs), and the stanza key is
  * `html` for a track and `htmlPath` for an assembly. Both producers write an
- * escaped anchor rather than a bare url, so the href comes back through a parse
- * rather than a regex.
+ * escaped anchor for a hub's page, so the href comes back through a parse. The
+ * converter writes golden-path assemblies' pages inline, and only under `ucsc`
+ * is markup read as a page, so a track's own `html` column stays a column.
+ *
+ * A url is http(s) only: it reaches `openLocation` and an anchor's href.
+ * `path` names the key read, which the metadata card leaves out.
  */
-export function getDescriptionHtmlUrl(metadata) {
-    return [metadata, isRecord(metadata) ? metadata.ucsc : undefined]
-        .flatMap(record => (isRecord(record) ? [record.html, record.htmlPath] : []))
-        .filter(candidate => typeof candidate === 'string')
-        .map(candidate => descriptionUrl(candidate))
-        .find(url => url !== undefined);
+export function findTrackDescription(metadata) {
+    const ucsc = isRecord(metadata) ? metadata.ucsc : undefined;
+    const places = [
+        { record: metadata, prefix: [], inline: false },
+        { record: ucsc, prefix: ['ucsc'], inline: true },
+    ];
+    for (const { record, prefix, inline } of places) {
+        for (const key of ['html', 'htmlPath']) {
+            const value = isRecord(record) ? record[key] : undefined;
+            const description = typeof value === 'string' ? parseDescription(value, inline) : undefined;
+            if (description) {
+                return { description, path: [...prefix, key] };
+            }
+        }
+    }
+    return undefined;
+}
+export function getTrackDescription(metadata) {
+    return findTrackDescription(metadata)?.description;
+}
+/**
+ * `metadata` without the key its description came from, since the Description
+ * card shows that one.
+ */
+export function omitTrackDescription(metadata) {
+    const path = findTrackDescription(metadata)?.path;
+    if (!path) {
+        return metadata;
+    }
+    const [key = '', nestedKey] = path;
+    const nested = metadata[key];
+    return nestedKey !== undefined && isRecord(nested)
+        ? { ...metadata, [key]: without(nested, nestedKey) }
+        : without(metadata, key);
+}
+function without(record, key) {
+    return Object.fromEntries(Object.entries(record).filter(([k]) => k !== key));
 }
 function absolute(value, baseUrl) {
     try {
@@ -38,8 +91,8 @@ function absolute(value, baseUrl) {
     }
 }
 /**
- * A fetched description page as markup for `SanitizedHTML`: links and images
- * resolved against the page they came from rather than the JBrowse origin, and
+ * A description page as markup for `SanitizedHTML`: links and images resolved
+ * against the page they came from rather than the JBrowse origin, and
  * `<form>` dropped, which the sanitizer keeps and which in a document off a
  * third-party origin is a credential prompt wearing the app's own chrome.
  *

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.11",
   "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": "^6.6.1",
+    "@jbrowse/mobx-state-tree": "^6.7.0",
     "@mui/icons-material": "^9.4.0",
     "@mui/material": "^9.4.0",
     "mobx": "^7.0.5",
     "mobx-react": "^10.0.2",
-    "@jbrowse/core": "^5.0.0-beta.10",
-    "@jbrowse/render-core": "^5.0.0-beta.10"
+    "@jbrowse/render-core": "^5.0.0-beta.11",
+    "@jbrowse/core": "^5.0.0-beta.11"
   },
   "peerDependencies": {
     "react": ">=19.0.0",