@jbrowse/core 5.0.0-beta.11 → 5.0.0-beta.13

package/esm/util/types/index.d.ts

@@ -1,6 +1,6 @@
 import type { ViewSnapshotInput } from '../../PluginManager.ts';
 import type TextSearchManager from '../../TextSearch/TextSearchManager.ts';
-import type { AnyConfigurationModel } from '../../configuration/index.ts';
+import type { AnyConfigurationModel, AnyTrackConfig, TrackConfigEntry } from '../../configuration/index.ts';
 import type { BaseInternetAccountModel, BaseTrackConfig } from '../../pluggableElementTypes/models/index.ts';
 import type { PluginDefinition } from '../../pluginDefinitions.ts';
 import type RpcManager from '../../rpc/RpcManager.ts';
@@ -53,17 +53,17 @@ export type AnimationMode = 'system' | 'enabled' | 'disabled';
  * in `./services.ts`, which is the file that stays cheap to name.
  */
 export interface TrackCatalog {
-    tracks: AnyConfigurationModel[];
+    tracks: TrackConfigEntry[];
     assemblies: AnyConfigurationModel[];
     connectionInstances?: {
         tracks: AnyConfigurationModel[];
     }[];
-    getTrackById: (id: string) => AnyConfigurationModel | undefined;
+    getTrackById: (id: string) => AnyTrackConfig | undefined;
 }
 /** minimum interface that all session state models must implement */
 export interface AbstractSessionModel extends AbstractViewContainer, RenderingServices, NotificationSink, DialogHost, TrackCatalog {
     /** @deprecated prefer the per-id reactive `getTrackById(id)` */
-    getTracksById: () => Record<string, AnyConfigurationModel>;
+    getTracksById: () => Record<string, AnyTrackConfig>;
     jbrowse: IAnyStateTreeNode;
     drawerPosition?: DrawerPosition;
     stickyViewHeaders?: boolean;
@@ -112,8 +112,8 @@ export interface AbstractSessionModel extends AbstractViewContainer, RenderingSe
         config: BaseTrackConfig;
         view?: TrackActionView;
     }) => MenuItem[];
-    getTrackActions?: (arg: BaseTrackConfig, view?: TrackActionView) => MenuItem[];
-    getTrackListMenuItems?: (arg: BaseTrackConfig, view?: TrackActionView) => MenuItem[];
+    getTrackActions?: (arg: AnyTrackConfig, view?: TrackActionView) => MenuItem[];
+    getTrackListMenuItems?: (arg: AnyTrackConfig, view?: TrackActionView) => MenuItem[];
     addAssembly?: (conf: Record<string, unknown>) => void;
     addSessionAssembly?: (conf: Record<string, unknown>) => void;
     sessionAssemblies?: AnyConfigurationModel[];
@@ -184,6 +184,14 @@ export interface SessionWithEditableTrackConfig extends AbstractSessionModel {
     getEditableTrackConfig(trackId: string, schemaType: IAnyType): AnyConfigurationModel | undefined;
 }
 export declare function isSessionWithEditableTrackConfig(t: unknown): t is SessionWithEditableTrackConfig;
+/**
+ * The working copy `trackId` resolves to (ADR-032), through its track type's
+ * own schema, which is the one a shown track's `configuration` reference
+ * holds, so both reach one node. Re-resolves on every read: an undo or a
+ * session restore replaces the working copy. Undefined when the session keeps
+ * no working copies or nothing answers the id.
+ */
+export declare function getEditableTrackConfigById(session: unknown, trackId: string): AnyConfigurationModel | undefined;
 /**
  * abstract interface for a session that keeps a list of views, so that `addView`
  * appends and the view a launch came out of survives it.
@@ -304,7 +312,7 @@ export interface SessionWithAddAssembly extends AbstractSessionModel {
 export declare function isSessionWithAddAssembly(t: unknown): t is SessionWithAddAssembly;
 /** abstract interface for a session that allows deleting track configs */
 export interface SessionWithDeleteTrackConf extends AbstractSessionModel {
-    deleteTrackConf(configuration: AnyConfigurationModel): void;
+    deleteTrackConf(configuration: AnyTrackConfig): void;
 }
 export declare function isSessionWithDeleteTrackConf(t: unknown): t is SessionWithDeleteTrackConf;
 /** abstract interface for a session allows adding tracks */

package/esm/util/types/index.js

@@ -1,4 +1,4 @@
-import { isStateTreeNode } from '@jbrowse/mobx-state-tree';
+import { getEnv, isStateTreeNode } from '@jbrowse/mobx-state-tree';
 import { isSessionServices } from './services.js';
 export { isSessionServices } from './services.js';
 // The plain-data half of this file's former self, kept re-exported here so
@@ -24,6 +24,23 @@ export function isSessionWithBaseTrackConfig(t) {
 export function isSessionWithEditableTrackConfig(t) {
     return isSessionModel(t) && 'getEditableTrackConfig' in t;
 }
+/**
+ * The working copy `trackId` resolves to (ADR-032), through its track type's
+ * own schema, which is the one a shown track's `configuration` reference
+ * holds, so both reach one node. Re-resolves on every read: an undo or a
+ * session restore replaces the working copy. Undefined when the session keeps
+ * no working copies or nothing answers the id.
+ */
+export function getEditableTrackConfigById(session, trackId) {
+    if (!isSessionWithEditableTrackConfig(session)) {
+        return undefined;
+    }
+    const type = session.getTrackById(trackId)?.type;
+    const schema = typeof type === 'string'
+        ? getEnv(session).pluginManager.getTrackType(type).configSchema
+        : undefined;
+    return schema ? session.getEditableTrackConfig(trackId, schema) : undefined;
+}
 export function isSessionWithMultipleViews(t) {
     return isSessionModel(t) && isStateTreeNode(t.views);
 }
@@ -106,7 +123,9 @@ export function isSessionModelWithConnections(thing) {
     return isSessionModel(thing) && 'makeConnection' in thing;
 }
 export function isSessionModelWithConnectionEditing(thing) {
-    return isSessionModel(thing) && 'addConnectionConf' in thing;
+    return (isSessionModel(thing) &&
+        'addConnectionConf' in thing &&
+        !('disableAddTracks' in thing && thing.disableAddTracks));
 }
 export function isSessionWithSessionPlugins(thing) {
     return isSessionModel(thing) && 'sessionPlugins' in thing;

package/esm/util/useRowVirtualScroll.d.ts

@@ -1,4 +1,5 @@
 import type { RowResizeTarget } from './applyRowResizeWheel.ts';
+export type { RowResizeTarget } from './applyRowResizeWheel.ts';
 /**
  * Wheel gestures over a **row-stack** panel — the multi-sample variant displays
  * and MAF: `shift`+wheel resizes the rows, keeping the row under the cursor

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "5.0.0-beta.11",
+  "version": "5.0.0-beta.13",
   "type": "module",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
@@ -130,6 +130,7 @@
     "./ui/Snackbar": "./esm/ui/Snackbar.js",
     "./ui/SnackbarModel": "./esm/ui/SnackbarModel.js",
     "./ui/StackTraceButton": "./esm/ui/StackTraceButton.js",
+    "./ui/SubmitDialog": "./esm/ui/SubmitDialog.js",
     "./ui/SvgColorLegend": "./esm/ui/SvgColorLegend.js",
     "./ui/VerticalScrollbar": "./esm/ui/VerticalScrollbar.js",
     "./ui/buildExtraTrackMenuItems": "./esm/ui/buildExtraTrackMenuItems.js",
@@ -161,6 +162,7 @@
     "./util/adapterMetadata": "./esm/util/adapterMetadata.js",
     "./util/addRelativeUris": "./esm/util/addRelativeUris.js",
     "./util/aggregateFieldName": "./esm/util/aggregateFieldName.js",
+    "./util/alignedBytes": "./esm/util/alignedBytes.js",
     "./util/analytics": "./esm/util/analytics.js",
     "./util/animationAllowed": "./esm/util/animationAllowed.js",
     "./util/assemblyConfigUtils": "./esm/util/assemblyConfigUtils.js",
@@ -217,6 +219,7 @@
     "./util/io/RemoteFileWithRangeCache": "./esm/util/io/RemoteFileWithRangeCache.js",
     "./util/isDataCurrent": "./esm/util/isDataCurrent.js",
     "./util/isTextEntryFocused": "./esm/util/isTextEntryFocused.js",
+    "./util/isoformRank": "./esm/util/isoformRank.js",
     "./util/jexl": "./esm/util/jexl.js",
     "./util/jexlFilters": "./esm/util/jexlFilters.js",
     "./util/jexlStrings": "./esm/util/jexlStrings.js",
@@ -314,12 +317,12 @@
     "dompurify": "^3.4.16",
     "generic-filehandle2": "^2.5.0",
     "idb": "^8.0.3",
-    "mobx": "^7.0.5",
+    "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
     "rxjs": "^7.8.2",
     "source-map-js": "^1.2.2",
-    "@jbrowse/add-track-core": "^5.0.0-beta.11",
-    "@jbrowse/render-core": "^5.0.0-beta.11"
+    "@jbrowse/add-track-core": "^5.0.0-beta.13",
+    "@jbrowse/render-core": "^5.0.0-beta.13"
   },
   "peerDependencies": {
     "react": ">=19.0.0",

package/esm/rpc/methods/CoreLoadAdapterCode.d.ts

@@ -1,13 +0,0 @@
-import RpcMethodType from '../../pluggableElementTypes/RpcMethodType.ts';
-import type { RpcExecuteArgs } from '../RpcRegistry.ts';
-/**
- * Load these adapter types' code in the worker a track is about to use. An
- * adapter's class arrives by dynamic import on the track's first request
- * otherwise, and that download waits for the view to lay out and the assembly
- * to load.
- */
-export default class CoreLoadAdapterCode extends RpcMethodType<'CoreLoadAdapterCode'> {
-    name: 'CoreLoadAdapterCode';
-    execute({ adapterTypes }: RpcExecuteArgs<'CoreLoadAdapterCode'>): Promise<void>;
-    serializeArguments(args: Record<string, unknown>): Promise<Record<string, unknown>>;
-}

package/esm/rpc/methods/CoreLoadAdapterCode.js

@@ -1,16 +0,0 @@
-import RpcMethodType from '../../pluggableElementTypes/RpcMethodType.js';
-/**
- * Load these adapter types' code in the worker a track is about to use. An
- * adapter's class arrives by dynamic import on the track's first request
- * otherwise, and that download waits for the view to lay out and the assembly
- * to load.
- */
-export default class CoreLoadAdapterCode extends RpcMethodType {
-    name = 'CoreLoadAdapterCode';
-    async execute({ adapterTypes }) {
-        await Promise.all(adapterTypes.map(type => this.pluginManager.getAdapterType(type).getAdapterClass()));
-    }
-    async serializeArguments(args) {
-        return args;
-    }
-}