@jbrowse/product-core 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/Session/pluginExtraTrackItems.js

@@ -0,0 +1,13 @@
+import { buildExtraTrackMenuItems } from '@jbrowse/core/ui/buildExtraTrackMenuItems';
+/**
+ * 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 function pluginExtraTrackItems(pluginManager, session, config, view) {
+    return buildExtraTrackMenuItems(pluginManager, {
+        session: session,
+        config,
+        view,
+    });
+}

package/esm/controllerTracks.d.ts

@@ -3,9 +3,10 @@ import type { LooseTrackInput } from '@jbrowse/core/util/tracks';
 import type { IStateTreeNode } from '@jbrowse/mobx-state-tree';
 export type TrackConf = Record<string, unknown>;
 /**
- * What a controller accepts per track: a full config, a bare data-file URL, or
- * `{ uri, index?, ...extra }`. The loose forms expand through core's
- * `guessTrackConf`, the same inference the "Add track" flow runs.
+ * What a controller accepts per track: a full config, the trackId of one the
+ * catalog already holds (a hub's, when the assembly came from one), a bare
+ * data-file URL, or `{ uri, index?, ...extra }`. The loose forms expand through
+ * core's `guessTrackConf`, the same inference the "Add track" flow runs.
  */
 export type TrackInput = string | TrackConf;
 interface ControllerView {
@@ -34,10 +35,11 @@ export declare function isLooseTrack(track: TrackInput): track is string | Loose
 export declare function withAssemblyName(track: TrackConf, assemblyName?: string): TrackConf;
 /**
  * Expand every loose entry into a full track config; stamp the assembly name
- * onto the ones already written out. `node` is any node of the live tree — the
- * pluginManager whose format plugins drive the guess comes off its env.
+ * onto the ones already written out. A string the catalog already resolves is
+ * that track, and is tried before the file guess: "not URL-shaped" cannot tell
+ * an id from a relative path like `data/reads.bam`.
  */
-export declare function resolveTracks(tracks: TrackInput[], node: IStateTreeNode, assemblyName?: string, localFiles?: Record<string, BlobLocation>): TrackConf[];
+export declare function resolveTracks(tracks: TrackInput[], session: ControllerSession, assemblyName?: string, localFiles?: Record<string, BlobLocation>): TrackConf[];
 /**
  * Register each track config only if the session cannot already resolve it, then
  * show it. `getTrackById` resolves catalog + connection + session tracks, so a
@@ -51,6 +53,9 @@ export declare function resolveTracks(tracks: TrackInput[], node: IStateTreeNode
 export declare function openTracks(session: ControllerSession, tracks: TrackConf[]): Promise<void>;
 /** Open every wanted track and close any others the view currently shows. */
 export declare function reconcileTracks(session: ControllerSession, tracks: TrackConf[]): Promise<void>;
-/** Merge a hub's own search adapters with the ones the caller supplied. */
-export declare function mergeSearchAdapters<T>(a: readonly T[] | undefined, b: readonly T[] | undefined): T[] | undefined;
+/**
+ * A hub's entries followed by the host's own, the host's winning where both
+ * carry the same `idKey`.
+ */
+export declare function withHostOverrides<T extends object>(hub: readonly T[] | undefined, host: readonly T[] | undefined, idKey: string): T[];
 export {};

package/esm/controllerTracks.js

@@ -1,4 +1,5 @@
 import { getEnv } from '@jbrowse/core/util';
+import { withPageBaseUri } from '@jbrowse/core/util/addRelativeUris';
 import { guessTrackConf } from '@jbrowse/core/util/tracks';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { resolveLocalFileUris } from './localFiles.js';
@@ -20,12 +21,16 @@ export function withAssemblyName(track, assemblyName) {
 }
 /**
  * Expand every loose entry into a full track config; stamp the assembly name
- * onto the ones already written out. `node` is any node of the live tree — the
- * pluginManager whose format plugins drive the guess comes off its env.
+ * onto the ones already written out. A string the catalog already resolves is
+ * that track, and is tried before the file guess: "not URL-shaped" cannot tell
+ * an id from a relative path like `data/reads.bam`.
  */
-export function resolveTracks(tracks, node, assemblyName, localFiles) {
-    const { pluginManager } = getEnv(node);
+export function resolveTracks(tracks, session, assemblyName, localFiles) {
+    const { pluginManager } = getEnv(session);
     return tracks.map(track => {
+        if (typeof track === 'string' && session.getTrackById(track)) {
+            return { trackId: track };
+        }
         const conf = isLooseTrack(track)
             ? guessTrackConf(track, pluginManager, assemblyName)
             : // full configs are stamped here too, not just in the build() catalog
@@ -35,7 +40,7 @@ export function resolveTracks(tracks, node, assemblyName, localFiles) {
                 withAssemblyName(track, assemblyName);
         // after the guess, so the adapter has already derived its index sibling
         // from the uri string and both get swapped for blobs together
-        return localFiles ? resolveLocalFileUris(conf, localFiles) : conf;
+        return withPageBaseUri(localFiles ? resolveLocalFileUris(conf, localFiles) : conf);
     });
 }
 /**
@@ -83,8 +88,12 @@ export async function reconcileTracks(session, tracks) {
         view.hideTrack(trackId);
     }
 }
-/** Merge a hub's own search adapters with the ones the caller supplied. */
-export function mergeSearchAdapters(a, b) {
-    const merged = [...(a ?? []), ...(b ?? [])];
-    return merged.length ? merged : undefined;
+/**
+ * A hub's entries followed by the host's own, the host's winning where both
+ * carry the same `idKey`.
+ */
+export function withHostOverrides(hub = [], host = [], idKey) {
+    const idOf = (entry) => entry[idKey];
+    const hostIds = new Set(host.map(idOf).filter(id => id !== undefined));
+    return [...hub.filter(entry => !hostIds.has(idOf(entry))), ...host];
 }

package/esm/index.d.ts

@@ -3,10 +3,10 @@ export { asRoot, asSession } from './siblingCast.ts';
 export { scheduleDetachedDestroy } from '@jbrowse/core/util';
 export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './RootModel/index.ts';
 export type { BaseRootModel, BaseRootModelType, RootConfigurationSnapshot, RootModelWithInternetAccounts, RootModelWithInternetAccountsType, } from './RootModel/index.ts';
-export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';
-export type { AssertSessionModel, BaseSession, BaseSessionType, ConnectionTrackConfigEntry, EditableTrackConfig, PlainTrackConfig, ReferringNode, SessionWithConnections, SessionWithConnectionsType, SessionWithDrawerWidgets, SessionWithDrawerWidgetsType, SessionWithMultipleViews, SessionWithMultipleViewsType, SessionWithReferenceManagement, SessionWithReferenceManagementType, SessionWithSessionTracks, SessionWithSessionTracksType, SessionWithThemes, SessionWithThemesType, SessionWithTracks, SessionWithTracksType, } from './Session/index.ts';
-export { AboutDialog, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.ts';
-export type { PreferencesDialogSession, PreferencesPanelDescriptor, } from './ui/index.ts';
+export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, hydratedForms, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.ts';
+export type { AssertSessionModel, BaseSession, BaseSessionType, ConnectionTrackConfigEntry, EditableTrackConfig, HydratedForms, PlainTrackConfig, ReferringNode, SessionWithConnections, SessionWithConnectionsType, SessionWithDrawerWidgets, SessionWithDrawerWidgetsType, SessionWithMultipleViews, SessionWithMultipleViewsType, SessionWithReferenceManagement, SessionWithReferenceManagementType, SessionWithSessionTracks, SessionWithSessionTracksType, SessionWithThemes, SessionWithThemesType, SessionWithTracks, SessionWithTracksType, } from './Session/index.ts';
+export { AboutDialog, AppReadyMarker, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.ts';
+export type { AboutPanelProps, PreferencesDialogSession, PreferencesPanelDescriptor, } from './ui/index.ts';
 export { initializeWorker } from './rpcWorker.ts';
 export { toPluginLoadRecord } from './pluginInput.ts';
 export type { PluginInput } from './pluginInput.ts';
@@ -16,7 +16,7 @@ export { decodeSessionFromUrl, encodeSessionToUrl } from './sessionUrl.ts';
 export type { SessionSnapshot } from './sessionUrl.ts';
 export { mergeLocalFiles, normalizeAdapterSnapshots, registerLocalFiles, resolveLocalFileUris, } from './localFiles.ts';
 export type { LocalFileInput } from './localFiles.ts';
-export { isLooseTrack, mergeSearchAdapters, openTracks, reconcileTracks, resolveTracks, withAssemblyName, } from './controllerTracks.ts';
+export { isLooseTrack, openTracks, reconcileTracks, resolveTracks, withAssemblyName, withHostOverrides, } from './controllerTracks.ts';
 export type { ControllerSession, TrackConf, TrackInput, } from './controllerTracks.ts';
 export { resolveAssemblies, resolveAssembly } from './resolveAssemblies.ts';
 export type { AssemblyInput, ResolvedAssemblies } from './resolveAssemblies.ts';
@@ -26,6 +26,6 @@ export { getSessionSnapshot, observeSession } from './observeSession.ts';
 export type { SessionObservers, ViewLocation } from './observeSession.ts';
 export { MIGRATED_DISPLAY_INSTANCE_KEYS, migrateConfigSnapshot, migrateSessionSnapshot, } from './sessionMigrations/index.ts';
 export { DEFAULT_WEB_BASE_URL, analyzeWebPortability, buildWebExportUrl, filterSessionInPlace, planWebExport, } from './sessionUtils.ts';
-export type { AssemblySnapshot, DroppedSessionNode, HostedBaseConfig, NonPortableLocation, SelfContainedReason, TrackSnapshot, WebExportInput, WebExportPlan, WebPortabilityReport, } from './sessionUtils.ts';
+export type { AssemblySnapshot, DroppedSessionNode, HostedBase, HostedBaseConfig, NonPortableLocation, SelfContainedReason, TrackSnapshot, WebExportInput, WebExportPlan, WebPortabilityReport, } from './sessionUtils.ts';
 export { describeUnbuildableNodes, pruneUnbuildableNodes, } from './pruneUnbuildableNodes.ts';
 export type { HeldNode, UnbuildableNode } from './pruneUnbuildableNodes.ts';

package/esm/index.js

@@ -1,8 +1,8 @@
 export { asRoot, asSession } from './siblingCast.js';
 export { scheduleDetachedDestroy } from '@jbrowse/core/util';
 export { BaseRootModelFactory, FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, HierarchicalConfigSchemaFactory, InternetAccountsRootModelMixin, PreferencesConfigSchemaFactory, createConfigModel, exportSessionMenuItem, importSessionMenuItem, isRootModel, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './RootModel/index.js';
-export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
-export { AboutDialog, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.js';
+export { BaseSessionModel, ConnectionManagementSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, PreferencesSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, TrackMenuItemsSessionMixin, TrackMenuSessionMixin, TracksManagerSessionMixin, aboutTrackMenuItem, bakeSessionCascades, getShareableSessionSnapshot, copyTrackSnapshot, finalizeSession, hydratedForms, isBaseSession, isSession, isSessionWithConnections, isSessionWithDrawerWidgets, isSessionWithMultipleViews, isSessionWithReferenceManagement, isSessionWithThemes, isSessionWithTracks, pluginExtraTrackItems, trackActionItems, trackActionMenuItems, trackListMenuItems, } from './Session/index.js';
+export { AboutDialog, AppReadyMarker, Drawer, DrawerControls, DrawerHeader, DrawerWidget, DrawerWidgetSelector, ModalWidget, ModalWidgetAppBar, PreferencesDialog, WidgetBody, WidgetHeading, drawerGridTemplateColumns, } from './ui/index.js';
 export { initializeWorker } from './rpcWorker.js';
 export { toPluginLoadRecord } from './pluginInput.js';
 export { loadRuntimePlugins } from './loadPlugins.js';
@@ -13,7 +13,7 @@ export { decodeSessionFromUrl, encodeSessionToUrl } from './sessionUrl.js';
 export { mergeLocalFiles, normalizeAdapterSnapshots, registerLocalFiles, resolveLocalFileUris, } from './localFiles.js';
 // the track half of an imperative controller: loose track specs -> configs, and
 // opening exactly the wanted set
-export { isLooseTrack, mergeSearchAdapters, openTracks, reconcileTracks, resolveTracks, withAssemblyName, } from './controllerTracks.js';
+export { isLooseTrack, openTracks, reconcileTracks, resolveTracks, withAssemblyName, withHostOverrides, } from './controllerTracks.js';
 // hub names, sequence URIs and hub configs -> assembly configs, so every
 // product takes the same assembly vocabulary
 export { resolveAssemblies, resolveAssembly } from './resolveAssemblies.js';

package/esm/loadPlugins.d.ts

@@ -1,4 +1,4 @@
-import type { LoadedPlugin } from '@jbrowse/core/PluginLoader';
+import type { LoadedPlugin, ReExportRegistryLoader } from '@jbrowse/core/PluginLoader';
 import type { PluginDefinition } from '@jbrowse/core/pluginDefinitions';
 export interface LoadPluginsArgs {
     fetchESM?: (url: string) => Promise<LoadedPlugin>;
@@ -26,8 +26,13 @@ export interface LoadPluginsArgs {
  * a second copy beside its own; a product that does not bundle them — the
  * circular-genome-view build has neither MafViewer nor GWAS in its corePlugins —
  * must still fetch one a config names, or the config silently loses the plugin.
+ *
+ * `reExports` is the product's `reExports.generated.ts`, which serves every
+ * `@jbrowse` package the product bundles. Required for the same reason: a
+ * plugin handed core's map alone cannot read the rest.
  */
-export declare function loadRuntimePlugins(pluginDefinitions: PluginDefinition[], { dropVendored, jbrowseVersion, ...args }: LoadPluginsArgs & {
+export declare function loadRuntimePlugins(pluginDefinitions: PluginDefinition[], { dropVendored, jbrowseVersion, reExports, ...args }: LoadPluginsArgs & {
     dropVendored: boolean;
     jbrowseVersion: string;
+    reExports: ReExportRegistryLoader;
 }): Promise<never[] | import("@jbrowse/core/PluginLoader").PluginRecord[]>;

package/esm/loadPlugins.js

@@ -15,8 +15,12 @@ import { resolveStorePluginRefs } from '@jbrowse/core/util';
  * a second copy beside its own; a product that does not bundle them — the
  * circular-genome-view build has neither MafViewer nor GWAS in its corePlugins —
  * must still fetch one a config names, or the config silently loses the plugin.
+ *
+ * `reExports` is the product's `reExports.generated.ts`, which serves every
+ * `@jbrowse` package the product bundles. Required for the same reason: a
+ * plugin handed core's map alone cannot read the rest.
  */
-export async function loadRuntimePlugins(pluginDefinitions, { dropVendored, jbrowseVersion, ...args }) {
+export async function loadRuntimePlugins(pluginDefinitions, { dropVendored, jbrowseVersion, reExports, ...args }) {
     // Before dropVendoredPlugins, which matches on the UMD name a ref does not
     // carry until the store supplies it. `jbrowseVersion` is required rather than
     // defaulted so a product that forgets it fails to compile instead of quietly
@@ -35,7 +39,7 @@ export async function loadRuntimePlugins(pluginDefinitions, { dropVendored, jbro
     const base = args.baseUri ?? args.baseUrl;
     return toLoad.length
         ? new PluginLoader(toLoad, args)
-            .installGlobalReExports(window)
+            .installGlobalReExports(window, reExports)
             .load(base ?? window.location.href)
         : [];
 }

package/esm/resolveAssemblies.d.ts

@@ -4,6 +4,10 @@ export interface TextSearchAdapterConfig {
     [key: string]: unknown;
 }
 type SearchAdapters = TextSearchAdapterConfig[] | undefined;
+export interface HubTrackConfig {
+    trackId: string;
+    [key: string]: unknown;
+}
 /**
  * The shapes an assembly can take, discriminated at resolve time: a sequence
  * file URL (`'.../hg38.fa.gz'`, `.2bit`, ...) built into an assembly via
@@ -16,11 +20,23 @@ export interface ResolvedAssembly {
     assembly: AssemblyConfig;
     /** whatever search adapters the hub this came from carried */
     aggregateTextSearchAdapters?: SearchAdapters;
+    /**
+     * the hub's track catalog, which its search index names its hits against, so
+     * a host keeping the index keeps these too
+     */
+    tracks?: HubTrackConfig[];
 }
-export interface ResolvedAssemblies {
+export interface ResolvedAssemblies<Track extends object = HubTrackConfig, Index extends object = TextSearchAdapterConfig> {
     assemblies: AssemblyConfig[];
-    /** whatever search adapters the resolved hubs carried, merged */
-    aggregateTextSearchAdapters?: SearchAdapters;
+    /** the hubs' search adapters, then the host's own */
+    aggregateTextSearchAdapters?: (TextSearchAdapterConfig | Index)[];
+    /** the hubs' track catalogs, then the host's own tracks */
+    tracks?: (HubTrackConfig | Track)[];
+}
+/** What a host already has, to merge with what its hubs bring. */
+export interface HostCatalog<Track extends object, Index extends object> {
+    tracks?: readonly Track[];
+    aggregateTextSearchAdapters?: readonly Index[];
 }
 /** One assembly in any of the four accepted shapes. */
 export declare function resolveAssembly(input: AssemblyInput): Promise<ResolvedAssembly>;
@@ -29,16 +45,23 @@ export declare function resolveAssembly(input: AssemblyInput): Promise<ResolvedA
  * the same vocabulary the single-view one does — `['hg38', 'mm39']` as readily
  * as two hand-written configs.
  *
+ * A hub brings a track catalog and a search index that names hits by those
+ * tracks' ids, so both come back beside the assemblies. Pass the host's own
+ * `tracks` and `aggregateTextSearchAdapters` as `host` and they come back merged
+ * in, the host's winning an id, which makes spreading the result into
+ * `createApp`'s options correct:
+ *
+ * ```ts
+ * createApp(el, { ...options, ...(await resolveAssemblies(names, options)) })
+ * ```
+ *
+ * A key neither the hubs nor the host supplied is left out rather than set to
+ * `undefined`, so a spread never clears one.
+ *
  * Exported because the resolution is async and `createApp` is not: an engine
  * that resolved its own genomes would have to hand back a controller whose
- * `viewState` is undefined until the fetches land, which is most of what makes
- * the single-view controller four times the size. A host builds its options
+ * `viewState` is undefined until the fetches land. A host builds its options
  * asynchronously already (runtime plugins), so this belongs in that step.
- *
- * Without it every host reimplements it — jbrowse-anywidget carried a
- * line-for-line Python translation of core's hubUrl/fetchHub/addRelativeUris,
- * GenArk regex and all, purely because the multi-view product could not take a
- * hub name.
  */
-export declare function resolveAssemblies(inputs: AssemblyInput[]): Promise<ResolvedAssemblies>;
+export declare function resolveAssemblies<Track extends object = HubTrackConfig, Index extends object = TextSearchAdapterConfig>(inputs: AssemblyInput[], host?: HostCatalog<Track, Index>): Promise<ResolvedAssemblies<Track, Index>>;
 export {};

package/esm/resolveAssemblies.js

@@ -1,5 +1,6 @@
 import { fetchHub } from '@jbrowse/core/util/fetchHub';
 import { isSequenceUri, makeAssembly } from '@jbrowse/core/util/makeAssembly';
+import { withHostOverrides } from './controllerTracks.js';
 // A hub's config arrives off the network, so its search adapters are untyped
 // there. Keep the ones that carry the id everything downstream references,
 // rather than casting the lot: an entry without one cannot be referred to by a
@@ -8,12 +9,20 @@ function searchAdaptersOf(hub) {
     const found = (hub.aggregateTextSearchAdapters ?? []).filter((a) => typeof a.textSearchAdapterId === 'string');
     return found.length ? found : undefined;
 }
+function tracksOf(hub) {
+    const found = (hub.tracks ?? []).filter((t) => typeof t.trackId === 'string');
+    return found.length ? found : undefined;
+}
 function fromHubConfig(hub) {
     const assembly = hub.assemblies?.[0];
     if (!assembly) {
         throw new Error('hub config has no assemblies');
     }
-    return { assembly, aggregateTextSearchAdapters: searchAdaptersOf(hub) };
+    return {
+        assembly,
+        aggregateTextSearchAdapters: searchAdaptersOf(hub),
+        tracks: tracksOf(hub),
+    };
 }
 /** One assembly in any of the four accepted shapes. */
 export async function resolveAssembly(input) {
@@ -34,22 +43,31 @@ export async function resolveAssembly(input) {
  * the same vocabulary the single-view one does — `['hg38', 'mm39']` as readily
  * as two hand-written configs.
  *
+ * A hub brings a track catalog and a search index that names hits by those
+ * tracks' ids, so both come back beside the assemblies. Pass the host's own
+ * `tracks` and `aggregateTextSearchAdapters` as `host` and they come back merged
+ * in, the host's winning an id, which makes spreading the result into
+ * `createApp`'s options correct:
+ *
+ * ```ts
+ * createApp(el, { ...options, ...(await resolveAssemblies(names, options)) })
+ * ```
+ *
+ * A key neither the hubs nor the host supplied is left out rather than set to
+ * `undefined`, so a spread never clears one.
+ *
  * Exported because the resolution is async and `createApp` is not: an engine
  * that resolved its own genomes would have to hand back a controller whose
- * `viewState` is undefined until the fetches land, which is most of what makes
- * the single-view controller four times the size. A host builds its options
+ * `viewState` is undefined until the fetches land. A host builds its options
  * asynchronously already (runtime plugins), so this belongs in that step.
- *
- * Without it every host reimplements it — jbrowse-anywidget carried a
- * line-for-line Python translation of core's hubUrl/fetchHub/addRelativeUris,
- * GenArk regex and all, purely because the multi-view product could not take a
- * hub name.
  */
-export async function resolveAssemblies(inputs) {
+export async function resolveAssemblies(inputs, host = {}) {
     const resolved = await Promise.all(inputs.map(resolveAssembly));
-    const adapters = resolved.flatMap(r => r.aggregateTextSearchAdapters ?? []);
+    const tracks = withHostOverrides(resolved.flatMap(r => r.tracks ?? []), host.tracks, 'trackId');
+    const adapters = withHostOverrides(resolved.flatMap(r => r.aggregateTextSearchAdapters ?? []), host.aggregateTextSearchAdapters, 'textSearchAdapterId');
     return {
         assemblies: resolved.map(r => r.assembly),
-        aggregateTextSearchAdapters: adapters.length ? adapters : undefined,
+        ...(tracks.length ? { tracks } : {}),
+        ...(adapters.length ? { aggregateTextSearchAdapters: adapters } : {}),
     };
 }

package/esm/rpcWorker.d.ts

@@ -1,11 +1,21 @@
 import { RpcServer } from '@jbrowse/core/util/librpc';
 import type { PluginConstructor } from '@jbrowse/core/Plugin';
-import type { LoadedPlugin } from '@jbrowse/core/PluginLoader';
+import type { LoadedPlugin, ReExportRegistryLoader } from '@jbrowse/core/PluginLoader';
 declare global {
     interface Window {
         rpcServer?: RpcServer;
     }
 }
+export interface WorkerOptions {
+    fetchESM?: (url: string) => Promise<LoadedPlugin>;
+    fetchCJS?: (url: string) => Promise<LoadedPlugin>;
+    /**
+     * The product's `workerReExports.generated.ts`, so a runtime plugin loading
+     * here reads the host's copy of every `@jbrowse` package the product
+     * bundles.
+     */
+    reExports: ReExportRegistryLoader;
+}
 type RpcFunc = (args: unknown) => Promise<unknown>;
 /**
  * Wire the method's `statusCallback` to the status channel the driver opened
@@ -31,8 +41,5 @@ type RpcFunc = (args: unknown) => Promise<unknown>;
  * about the driver on the other side of postMessage that nothing else asserts.
  */
 export declare function wrapForRpc(func: RpcFunc): (args: unknown) => Promise<unknown>;
-export declare function initializeWorker(corePlugins: PluginConstructor[], opts: {
-    fetchESM?: (url: string) => Promise<LoadedPlugin>;
-    fetchCJS?: (url: string) => Promise<LoadedPlugin>;
-}): Promise<void>;
+export declare function initializeWorker(corePlugins: PluginConstructor[], opts: WorkerOptions): Promise<void>;
 export {};

package/esm/rpcWorker.js

@@ -31,7 +31,7 @@ async function getPluginManager(corePlugins, opts) {
     // engine — needs its definition here, not just its instance.
     const runtimePlugins = config.plugins.length
         ? await new PluginLoader(config.plugins, opts)
-            .installGlobalReExports(self)
+            .installGlobalReExports(self, opts.reExports)
             .load(config.windowHref)
         : [];
     return new PluginManager([

package/esm/sessionMigrations/index.d.ts

@@ -12,7 +12,7 @@
  *   LinearFeatureDisplay → LinearBasicDisplay
  *
  * Also lifts the per-instance alignments settings a v4.3.0 session persisted
- * (`colorBySetting`, `filterBySetting`, `jexlFilters`, `trackMaxHeight`,
+ * (`colorBySetting`, `filterBySetting`, `trackMaxHeight`,
  * `hideMismatchesSetting`) into the config where they now live as slots — off
  * the nested `LinearAlignmentsDisplay` container's `PileupDisplay` /
  * `SNPCoverageDisplay` sub-nodes and off a flat old display alike, see
@@ -35,10 +35,10 @@
  * membership is whether the key still works, not which file makes it work.
  *
  * Keyed rather than flat because the same name means different things on
- * different displays: `jexlFilters` is lifted for the alignments display and,
- * differently, for the two variant ones, while on a LinearBasicDisplay — whose
- * own prop has always been `jexlFiltersSetting` — it is simply dead, and a flat
- * list would call that one supported.
+ * different displays: `jexlFilters` still works on the two multi-sample variant
+ * ones, while on a LinearBasicDisplay — whose own prop has always been
+ * `jexlFiltersSetting` — and on the alignments display, which reads no filter
+ * slot at all, it is simply dead, and a flat list would call those supported.
  */
 export declare const MIGRATED_DISPLAY_INSTANCE_KEYS: Record<string, string[]>;
 /**

package/esm/sessionMigrations/index.js

@@ -12,7 +12,7 @@
  *   LinearFeatureDisplay → LinearBasicDisplay
  *
  * Also lifts the per-instance alignments settings a v4.3.0 session persisted
- * (`colorBySetting`, `filterBySetting`, `jexlFilters`, `trackMaxHeight`,
+ * (`colorBySetting`, `filterBySetting`, `trackMaxHeight`,
  * `hideMismatchesSetting`) into the config where they now live as slots — off
  * the nested `LinearAlignmentsDisplay` container's `PileupDisplay` /
  * `SNPCoverageDisplay` sub-nodes and off a flat old display alike, see
@@ -62,6 +62,58 @@ const displayTypeMap = {
 // modifications/methylation session opens colored `normal`). We pull them off
 // the instance here and route them into the config.
 const NESTED_ALIGNMENTS_SUBNODES = ['PileupDisplay', 'SNPCoverageDisplay'];
+// The alignments `color` field each v4 scheme name paints now. `methylation`,
+// `stranded` and `insertSizeGradient` were retired before the colour object
+// and land on the fields that replaced them.
+const V4_COLOR_FIELDS = {
+    strand: 'strand',
+    mappingQuality: 'mapq',
+    insertSize: 'insertSize',
+    insertSizeGradient: 'insertSize',
+    firstOfPairStrand: 'firstOfPairStrand',
+    stranded: 'firstOfPairStrand',
+    pairOrientation: 'pairOrientation',
+    insertSizeAndOrientation: 'insertSizeAndOrientation',
+    mateRefName: 'mateRefName',
+};
+// The v4 schemes that drew a cell per base, which are the `baseColor` object's
+// field now rather than the read fill's.
+const V4_BASE_COLOR_FIELDS = {
+    perBaseQuality: 'baseQuality',
+    perBaseLetter: 'base',
+    perBaseLettering: 'base',
+    modifications: 'modifications',
+    methylation: 'modifications',
+    bisulfite: 'bisulfite',
+};
+function colorSlotsOf(value) {
+    if (!isObject(value)) {
+        return {};
+    }
+    const { type, tag, modifications } = value;
+    const field = type === 'tag' && typeof tag === 'string'
+        ? `tags.${tag}`
+        : typeof type === 'string'
+            ? V4_COLOR_FIELDS[type]
+            : undefined;
+    const baseField = typeof type === 'string' ? V4_BASE_COLOR_FIELDS[type] : undefined;
+    const given = isObject(modifications) ? modifications : undefined;
+    const { isolatedModification, ...rest } = given ?? {};
+    const settings = given || type === 'methylation'
+        ? {
+            ...rest,
+            ...(typeof isolatedModification === 'string'
+                ? { shownModifications: [isolatedModification] }
+                : {}),
+            ...(type === 'methylation' ? { fillUnmarked: true } : {}),
+        }
+        : undefined;
+    return {
+        ...(field ? { color: { field } } : {}),
+        ...(baseField ? { baseColor: { field: baseField } } : {}),
+        ...(settings ? { modifications: settings } : {}),
+    };
+}
 // Persisted key -> the slot it now lives in, and how to carry its value across.
 //
 // The `*Setting` names are the ones a real saved session carries, and getting
@@ -74,13 +126,19 @@ const NESTED_ALIGNMENTS_SUBNODES = ['PileupDisplay', 'SNPCoverageDisplay'];
 //
 // `hideSmallIndelsSetting` and `hideLargeIndelsSetting` are deliberately absent:
 // those two toggles have no slot today, the feature having been removed rather
-// than moved, so there is nowhere to carry them.
+// than moved, so there is nowhere to carry them. `jexlFilters` is absent for the
+// same reason since the slot left `baseLinearDisplayConfigSchema`: the
+// alignments display never read it, so the slot this used to carry the value to
+// no longer exists.
+//
+// `spread` carries one old key across as several slots: a v4 `colorBy` named a
+// scheme and held the modification settings, which are the `color` or
+// `baseColor` object's field and the `modifications` slot now.
 const MIGRATED_INSTANCE_SLOTS = {
-    colorBy: { slot: 'colorBy' },
-    colorBySetting: { slot: 'colorBy' },
+    colorBy: { slot: 'color', spread: colorSlotsOf },
+    colorBySetting: { slot: 'color', spread: colorSlotsOf },
     filterBy: { slot: 'filterBy' },
     filterBySetting: { slot: 'filterBy' },
-    jexlFilters: { slot: 'jexlFilters' },
     trackMaxHeight: { slot: 'maxHeight' },
     hideMismatchesSetting: {
         slot: 'showMismatches',
@@ -102,10 +160,10 @@ const MIGRATED_INSTANCE_SLOTS = {
  * membership is whether the key still works, not which file makes it work.
  *
  * Keyed rather than flat because the same name means different things on
- * different displays: `jexlFilters` is lifted for the alignments display and,
- * differently, for the two variant ones, while on a LinearBasicDisplay — whose
- * own prop has always been `jexlFiltersSetting` — it is simply dead, and a flat
- * list would call that one supported.
+ * different displays: `jexlFilters` still works on the two multi-sample variant
+ * ones, while on a LinearBasicDisplay — whose own prop has always been
+ * `jexlFiltersSetting` — and on the alignments display, which reads no filter
+ * slot at all, it is simply dead, and a flat list would call those supported.
  */
 export const MIGRATED_DISPLAY_INSTANCE_KEYS = {
     '*': ['heightPreConfig'],
@@ -123,9 +181,14 @@ export const MIGRATED_DISPLAY_INSTANCE_KEYS = {
 // the display was actually writing.
 function migratedSettingsOf(source) {
     const settings = {};
-    for (const [key, { slot, convert }] of Object.entries(MIGRATED_INSTANCE_SLOTS)) {
+    for (const [key, { slot, convert, spread }] of Object.entries(MIGRATED_INSTANCE_SLOTS)) {
         if (source[key] !== undefined) {
-            settings[slot] = convert ? convert(source[key]) : source[key];
+            if (spread) {
+                Object.assign(settings, spread(source[key]));
+            }
+            else {
+                settings[slot] = convert ? convert(source[key]) : source[key];
+            }
         }
     }
     return settings;
@@ -133,12 +196,6 @@ function migratedSettingsOf(source) {
 function isObject(v) {
     return !!v && typeof v === 'object' && !Array.isArray(v);
 }
-// The standalone `methylation` colorBy scheme was removed; it is now the
-// `modifications` scheme with `fillUnmarked` set. It is NOT rewritten here: the
-// alignments model normalizes it at read time (`normalizeColorBy`, applied in
-// its `colorBy` getter), which covers every persistence path — instance slot and
-// config-file display default alike — so session migration deliberately leaves a
-// `methylation` colorBy untouched.
 function migrateDisplayType(display, trackConfigId, collected) {
     const entry = displayTypeMap[display.type];
     if (!entry) {
@@ -184,8 +241,10 @@ function migrateDisplayType(display, trackConfigId, collected) {
  *
  * The display's own keys are read only when it carries a `configuration`
  * reference, i.e. only for a session instance. A *config* display node reaches
- * this same function through `migrateConfigSnapshot`, and there `colorBy` and
- * friends are the live slots — lifting them would strip a working config.
+ * this same function through `migrateConfigSnapshot`, and there `filterBy` and
+ * friends are the live slots — lifting them would strip a working config. Its
+ * `colorBy` is the one key rewritten in place, onto the `color`, `baseColor`
+ * and `modifications` slots that replaced it.
  */
 function extractAlignmentsInstanceSettings(display, trackConfigId, collected) {
     if (display.type !== 'LinearAlignmentsDisplay') {
@@ -202,6 +261,10 @@ function extractAlignmentsInstanceSettings(display, trackConfigId, collected) {
         ...(subNode ? migratedSettingsOf(subNode) : {}),
         ...ownSettings,
     };
+    if (!isInstance && !subNode && display.colorBy !== undefined) {
+        const { colorBy, ...config } = display;
+        return { ...config, ...colorSlotsOf(colorBy) };
+    }
     if (!subNode && Object.keys(settings).length === 0) {
         return display;
     }

package/esm/sessionUrl.js

@@ -1,5 +1,5 @@
 import { ENCODED_PREFIX, fromUrlSafeB64, toUrlSafeB64, } from '@jbrowse/core/util';
-import { getShareableSessionSnapshot } from './Session/index.js';
+import { getShareableSessionSnapshot } from './Session/shareableSnapshot.js';
 /**
  * Serialize a live session into a compact, URL-safe string for a query param or
  * hash fragment. Deflated then base64url-encoded, so it survives a URL intact

package/esm/sessionUtils.d.ts

@@ -1,3 +1,4 @@
+import type { HydratedForms } from './Session/hydratedForms.ts';
 import type { PluginDefinition } from '@jbrowse/core/pluginDefinitions';
 import type { IAnyStateTreeNode, IAnyType } from '@jbrowse/mobx-state-tree';
 export interface DroppedSessionNode {
@@ -48,6 +49,10 @@ export interface HostedBaseConfig {
     };
     [key: string]: unknown;
 }
+export interface HostedBase {
+    config: HostedBaseConfig;
+    forms: HydratedForms;
+}
 export interface WebExportPlan {
     strategy: 'hostedConfigBase' | 'selfContained';
     configUrl?: string;
@@ -61,7 +66,7 @@ export interface WebExportPlan {
     unavailableAccounts: string[];
 }
 export type SelfContainedReason = 'noSourceConfig' | 'baseUnreachable' | 'assembliesNotInBase';
-export declare function planWebExport(snapshot: WebExportInput, baseConfig?: HostedBaseConfig): WebExportPlan;
+export declare function planWebExport(snapshot: WebExportInput, base?: HostedBase): WebExportPlan;
 export declare const DEFAULT_WEB_BASE_URL = "https://jbrowse.org/code/jb2/latest/";
 export declare function buildWebExportUrl(plan: Pick<WebExportPlan, 'webBaseUrl' | 'configUrl'>, sessionParam: string, options?: {
     password?: string;