@jbrowse/product-core 5.0.0-beta.7 → 5.0.0-beta.9

package/esm/ui/aboutTestUtils.d.ts

@@ -0,0 +1,140 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import type { SnapshotIn } from '@jbrowse/mobx-state-tree';
+export declare const aboutTestPluginManager: PluginManager;
+export declare const TestTrackConf: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    readonly name: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    readonly assemblyNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    readonly adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly type: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly bamLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    readonly metadata: {
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
+    };
+    readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly config: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly hideUris: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    trackId: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+export declare function makeTrackConf(snapshot: SnapshotIn<typeof TestTrackConf>): import("@jbrowse/core/configuration").ConfigNodeProps<{
+    readonly name: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    readonly assemblyNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    readonly adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly type: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly bamLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    readonly metadata: {
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
+    };
+    readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly config: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly hideUris: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    trackId: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+}> & import("@jbrowse/core/configuration").ConfigNodeActions & import("@jbrowse/core/configuration").ConfigNodeBrand<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    readonly name: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    readonly assemblyNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    readonly adapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly type: {
+            type: "string";
+        } & {
+            defaultValue: string;
+        };
+        readonly bamLocation: {
+            type: "fileLocation";
+        } & {
+            defaultValue: unknown;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    readonly metadata: {
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
+    };
+    readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly config: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly hideUris: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>;
+    trackId: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>>>>;

package/esm/ui/aboutTestUtils.js

@@ -0,0 +1,25 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import { ConfigurationSchema, FormatAboutConfigSchemaFactory, } from '@jbrowse/core/configuration';
+// a real PluginManager provides the jexl instance a callback slot evaluates with
+export const aboutTestPluginManager = new PluginManager([]).createPluggableElements();
+aboutTestPluginManager.configure();
+// the slots the About dialog reads off a track config, without registering a
+// track type to get them
+export const TestTrackConf = ConfigurationSchema('TestTrack', {
+    name: { type: 'string', defaultValue: '' },
+    assemblyNames: { type: 'stringArray', defaultValue: [] },
+    adapter: ConfigurationSchema('TestAdapter', {
+        type: { type: 'string', defaultValue: 'TestAdapter' },
+        bamLocation: {
+            type: 'fileLocation',
+            defaultValue: { uri: '', locationType: 'UriLocation' },
+        },
+    }),
+    metadata: { type: 'frozen', defaultValue: {} },
+    formatAbout: FormatAboutConfigSchemaFactory(),
+}, { explicitIdentifier: 'trackId' });
+export function makeTrackConf(snapshot) {
+    return TestTrackConf.create(snapshot, {
+        pluginManager: aboutTestPluginManager,
+    });
+}

package/esm/ui/descriptionHtml.d.ts

@@ -1,9 +1,8 @@
-import type { AboutConfig } from './util.ts';
 /**
- * The URL of a track's prose description page, 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.
+ * 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.
  *
  * Four spellings: `UCSCTrackHubConnection` spreads the trackDb stanza across
  * `metadata`, the bulk converter behind genomes.jbrowse.org nests it under
@@ -12,7 +11,7 @@ import type { AboutConfig } from './util.ts';
  * escaped anchor rather than a bare url, so the href comes back through a parse
  * rather than a regex.
  */
-export declare function getDescriptionHtmlUrl(config: AboutConfig): string | undefined;
+export declare function getDescriptionHtmlUrl(metadata: unknown): string | undefined;
 /**
  * A fetched description page as markup for `SanitizedHTML`: links and images
  * resolved against the page they came from rather than the JBrowse origin, and

package/esm/ui/descriptionHtml.js

@@ -1,4 +1,3 @@
-import { readConfSlot } from '@jbrowse/core/configuration';
 function isRecord(value) {
     return typeof value === 'object' && value !== null;
 }
@@ -11,10 +10,10 @@ function descriptionUrl(value) {
     return /^https?:\/\//i.test(candidate) ? candidate : undefined;
 }
 /**
- * The URL of a track's prose description page, 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.
+ * 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.
  *
  * Four spellings: `UCSCTrackHubConnection` spreads the trackDb stanza across
  * `metadata`, the bulk converter behind genomes.jbrowse.org nests it under
@@ -23,8 +22,7 @@ function descriptionUrl(value) {
  * escaped anchor rather than a bare url, so the href comes back through a parse
  * rather than a regex.
  */
-export function getDescriptionHtmlUrl(config) {
-    const metadata = readConfSlot(config, 'metadata');
+export function getDescriptionHtmlUrl(metadata) {
     return [metadata, isRecord(metadata) ? metadata.ucsc : undefined]
         .flatMap(record => (isRecord(record) ? [record.html, record.htmlPath] : []))
         .filter(candidate => typeof candidate === 'string')

package/esm/ui/index.d.ts

@@ -1,4 +1,6 @@
+export { default as AppReadyMarker } from './AppReadyMarker.tsx';
 export { default as AboutDialog } from './AboutDialog.tsx';
+export type { AboutPanelProps } from './util.ts';
 export { default as Drawer } from './Drawer.tsx';
 export { default as DrawerControls } from './DrawerControls.tsx';
 export { default as DrawerHeader } from './DrawerHeader.tsx';

package/esm/ui/index.js

@@ -1,3 +1,4 @@
+export { default as AppReadyMarker } from './AppReadyMarker.js';
 export { default as AboutDialog } from './AboutDialog.js';
 export { default as Drawer } from './Drawer.js';
 export { default as DrawerControls } from './DrawerControls.js';

package/esm/ui/util.d.ts

@@ -1,48 +1,30 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { AbstractSessionModel } from '@jbrowse/core/util';
-export type AboutConfig = AnyConfigurationModel | Record<string, unknown>;
 export interface AboutPanelProps {
     session: AbstractSessionModel;
-    config: AboutConfig;
+    /** the track's config, hydrated by the dialog before any panel sees it */
+    config: AnyConfigurationModel;
 }
 declare module '@jbrowse/core/PluginManager' {
     interface ExtensionPointRegistry {
         'Core-extraAboutPanel': ComponentList<AboutPanelProps>;
         /** #extensionPoint Core-replaceAbout | sync | Replace or wrap a track's About dialog body */
         'Core-replaceAbout': ComponentSlot<AboutPanelProps>;
-        'Core-customizeAbout': {
-            args: {
-                config: Record<string, unknown>;
-            };
-            result: {
-                config: {
-                    metadata?: Record<string, unknown>;
-                    [key: string]: unknown;
-                };
-            };
-            props: AboutPanelProps;
-        };
     }
 }
 /**
- * Build what a track's About dialog shows: the base config merged with session-
- * and track-level `formatAbout` overrides and passed through the
- * `Core-customizeAbout` extension point, plus the resolved `hideUris`.
- *
- * Both `formatAbout` slots are two-tier and resolve here together, so the
- * dialog reads one thing rather than re-deriving half the rule at the call
- * site. They fold differently on purpose: `config` is a merge the track can win
- * key-by-key, `hideUris` is an OR a track cannot turn back off.
+ * What a track's About dialog shows: the config with the session's and the
+ * track's `formatAbout` callbacks merged over it, plus the resolved `hideUris`.
+ * The two slots fold differently on purpose: `config` is a merge the track can
+ * win key-by-key, `hideUris` an OR a track cannot turn back off.
  */
-export declare function getAboutDialogConfig({ config, session, pluginManager, }: {
-    config: AboutConfig;
+export declare function getAboutDialogConfig({ config, session, }: {
+    config: AnyConfigurationModel;
     session: AbstractSessionModel;
-    pluginManager: PluginManager;
 }): {
     config: {
-        metadata?: Record<string, unknown>;
         [key: string]: unknown;
+        metadata?: Record<string, unknown>;
     };
     hideUris: boolean;
 };

package/esm/ui/util.js

@@ -1,39 +1,20 @@
-import { getConf, mergeFormatCallbacks, readConfObject, readConfSlot, } from '@jbrowse/core/configuration';
-import { isStateTreeNode } from '@jbrowse/mobx-state-tree';
+import { getConf, mergeFormatCallbacks, readConfObject, } from '@jbrowse/core/configuration';
 // #endregion
 /**
- * Build what a track's About dialog shows: the base config merged with session-
- * and track-level `formatAbout` overrides and passed through the
- * `Core-customizeAbout` extension point, plus the resolved `hideUris`.
- *
- * Both `formatAbout` slots are two-tier and resolve here together, so the
- * dialog reads one thing rather than re-deriving half the rule at the call
- * site. They fold differently on purpose: `config` is a merge the track can win
- * key-by-key, `hideUris` is an OR a track cannot turn back off.
+ * What a track's About dialog shows: the config with the session's and the
+ * track's `formatAbout` callbacks merged over it, plus the resolved `hideUris`.
+ * The two slots fold differently on purpose: `config` is a merge the track can
+ * win key-by-key, `hideUris` an OR a track cannot turn back off.
  */
-export function getAboutDialogConfig({ config, session, pluginManager, }) {
-    const conf = isStateTreeNode(config)
-        ? readConfObject(config)
-        : config;
-    const trackFormatAbout = readConfSlot(config, ['formatAbout', 'config'], { config: conf }, pluginManager.jexl);
-    const sessionFormatAbout = getConf(session, ['formatAbout', 'config'], {
-        config: conf,
-    });
-    // same two-tier merge the feature-details panel runs on `formatDetails`,
-    // session first so a track can override individual keys
-    const merged = {
-        config: {
-            ...conf,
-            ...mergeFormatCallbacks(sessionFormatAbout, trackFormatAbout),
-        },
+export function getAboutDialogConfig({ config, session, }) {
+    const conf = readConfObject(config);
+    const shown = {
+        ...conf,
+        ...mergeFormatCallbacks(getConf(session, ['formatAbout', 'config'], { config: conf }), readConfObject(config, ['formatAbout', 'config'], { config: conf })),
     };
     return {
-        ...pluginManager.evaluateExtensionPoint(
-        /** #extensionPoint Core-customizeAbout | sync | Transform the config shown in a track's About dialog */
-        'Core-customizeAbout', merged, { session, config }),
-        // OR'd, not merged: a deployment that hides file locations session-wide
-        // can't have a track turn them back on. Documented on the slot
+        config: shown,
         hideUris: Boolean(getConf(session, ['formatAbout', 'hideUris']) ||
-            readConfSlot(config, ['formatAbout', 'hideUris'])),
+            readConfObject(config, ['formatAbout', 'hideUris'])),
     };
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "5.0.0-beta.7",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
@@ -25,13 +25,13 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "@jbrowse/mobx-state-tree": "^6.5.2",
     "@mui/icons-material": "^9.4.0",
     "@mui/material": "^9.4.0",
     "mobx": "^7.0.3",
     "mobx-react": "^10.0.2",
-    "@jbrowse/core": "^5.0.0-beta.7",
-    "@jbrowse/render-core": "^5.0.0-beta.7"
+    "@jbrowse/render-core": "^5.0.0-beta.9",
+    "@jbrowse/core": "^5.0.0-beta.9"
   },
   "peerDependencies": {
     "react": ">=19.0.0",