@jbrowse/core 2.10.1 → 2.10.3

package/BaseFeatureWidget/stateModelFactory.js

@@ -0,0 +1,168 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.stateModelFactory = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mobx_1 = require("mobx");
+const clone_1 = __importDefault(require("clone"));
+const configuration_1 = require("../configuration");
+const util_1 = require("../util");
+const mst_1 = require("../util/types/mst");
+function formatSubfeatures(obj, depth, parse, currentDepth = 0, returnObj = {}) {
+    var _a;
+    if (depth <= currentDepth) {
+        return;
+    }
+    (_a = obj.subfeatures) === null || _a === void 0 ? void 0 : _a.map(sub => {
+        formatSubfeatures(sub, depth, parse, currentDepth + 1, returnObj);
+        parse(sub);
+    });
+}
+/**
+ * #stateModel BaseFeatureWidget
+ * displays data about features, allowing configuration callbacks to modify the
+ * contents of what is displayed
+ *
+ * see: formatDetails-\>feature,formatDetails-\>subfeatures
+ */
+function stateModelFactory(pluginManager) {
+    return mobx_state_tree_1.types
+        .model('BaseFeatureWidget', {
+        /**
+         * #property
+         */
+        id: mst_1.ElementId,
+        /**
+         * #property
+         */
+        type: mobx_state_tree_1.types.literal('BaseFeatureWidget'),
+        /**
+         * #property
+         */
+        featureData: mobx_state_tree_1.types.frozen(),
+        /**
+         * #property
+         */
+        formattedFields: mobx_state_tree_1.types.frozen(),
+        /**
+         * #property
+         */
+        unformattedFeatureData: mobx_state_tree_1.types.frozen(),
+        /**
+         * #property
+         */
+        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
+        /**
+         * #property
+         */
+        track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
+        /**
+         * #property
+         */
+        trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        /**
+         * #property
+         */
+        trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        /**
+         * #property
+         */
+        maxDepth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
+    })
+        .volatile(() => ({
+        error: undefined,
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        setFeatureData(featureData) {
+            self.unformattedFeatureData = featureData;
+        },
+        /**
+         * #action
+         */
+        clearFeatureData() {
+            self.featureData = undefined;
+        },
+        /**
+         * #action
+         */
+        setFormattedData(feat) {
+            self.featureData = feat;
+        },
+        /**
+         * #action
+         */
+        setExtra(type, trackId, maxDepth) {
+            self.trackId = trackId;
+            self.trackType = type;
+            self.maxDepth = maxDepth;
+        },
+        /**
+         * #action
+         */
+        setError(e) {
+            self.error = e;
+        },
+    }))
+        .actions(self => ({
+        afterCreate() {
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                try {
+                    const { unformattedFeatureData, track } = self;
+                    const session = (0, util_1.getSession)(self);
+                    if (track) {
+                        self.setExtra(track.type, track.configuration.trackId, (0, configuration_1.getConf)(track, ['formatDetails', 'maxDepth']));
+                    }
+                    if (unformattedFeatureData) {
+                        const feature = (0, clone_1.default)(unformattedFeatureData);
+                        const combine = (arg2, feature) => ({
+                            ...(0, configuration_1.getConf)(session, ['formatDetails', arg2], { feature }),
+                            ...(0, configuration_1.getConf)(track, ['formatDetails', arg2], { feature }),
+                        });
+                        if (track) {
+                            // eslint-disable-next-line no-underscore-dangle
+                            feature.__jbrowsefmt = combine('feature', feature);
+                            formatSubfeatures(feature, (0, configuration_1.getConf)(track, ['formatDetails', 'depth']), sub => {
+                                // eslint-disable-next-line no-underscore-dangle
+                                sub.__jbrowsefmt = combine('subfeatures', sub);
+                            });
+                        }
+                        self.setFormattedData(feature);
+                    }
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
+                }
+            }));
+        },
+    }))
+        .preProcessSnapshot(snap => {
+        // @ts-expect-error
+        const { featureData, finalizedFeatureData, ...rest } = snap;
+        return {
+            unformattedFeatureData: featureData,
+            featureData: finalizedFeatureData,
+            ...rest,
+        };
+    })
+        .postProcessSnapshot(snap => {
+        // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
+        const { unformattedFeatureData, featureData, ...rest } = snap;
+        // finalizedFeatureData avoids running formatter twice if loading from
+        // snapshot
+        return {
+            // replacing undefined with null helps with allowing fields to be
+            // hidden, setting null is not allowed by jexl so we set it to
+            // undefined to hide. see config guide. this replacement happens both
+            // here and when displaying the featureData in base feature widget
+            finalizedFeatureData: JSON.parse(JSON.stringify(featureData, (_, v) => (v === undefined ? null : v))),
+            ...rest,
+        };
+    });
+}
+exports.stateModelFactory = stateModelFactory;

package/Plugin.d.ts

@@ -9,6 +9,6 @@ export default abstract class Plugin {
     version?: string;
     install(_pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;
-    configurationSchema: AnyConfigurationSchemaType | undefined;
+    configurationSchema?: AnyConfigurationSchemaType;
 }
 export type PluginConstructor = new (...args: unknown[]) => Plugin;

package/Plugin.js

@@ -4,9 +4,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * base class for a JBrowse plugin
  */
 class Plugin {
-    constructor() {
-        this.configurationSchema = undefined;
-    }
     install(_pluginManager) { }
     configure(_pluginManager) { }
 }

package/ReExports/modules.js

@@ -180,7 +180,7 @@ const Entries = {
 };
 const LazyMUICore = Object.fromEntries(Object.entries(Entries).map(([key, ReactComponent]) => {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
         react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
     Component.displayName = key;
     return [key, Component];
@@ -353,21 +353,21 @@ const DataGridEntries = {
 };
 const LazyDataGridComponents = Object.fromEntries(Object.entries(DataGridEntries).map(([key, ReactComponent]) => {
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+    const Component = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
         react_1.default.createElement(ReactComponent, { ...props, ref: ref }))));
     Component.displayName = key;
     return [key, Component];
 }));
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-const LazyAttributes = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+const LazyAttributes = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
     react_1.default.createElement(Attributes, { ...props, ref: ref }))));
 LazyAttributes.displayName = 'Attributes';
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-const LazyFeatureDetails = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+const LazyFeatureDetails = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
     react_1.default.createElement(FeatureDetails, { ...props, ref: ref }))));
 LazyFeatureDetails.displayName = 'FeatureDetails';
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-const LazyBaseCard = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+const LazyBaseCard = react_1.default.forwardRef((props, ref) => (react_1.default.createElement(react_1.Suspense, { fallback: null },
     react_1.default.createElement(BaseCard, { ...props, ref: ref }))));
 LazyBaseCard.displayName = 'BaseCard';
 const libs = {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.10.1",
+  "version": "2.10.3",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -53,6 +53,7 @@
     "rbush": "^3.0.1",
     "react-error-boundary": "^4.0.3",
     "serialize-error": "^8.0.0",
+    "source-map-js": "^1.0.2",
     "svg-path-generator": "^1.1.0"
   },
   "peerDependencies": {
@@ -71,5 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "442b5f87efddfdf4ccf520b4d9dd01ddd370cb07"
+  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
 }

package/pluggableElementTypes/renderers/ServerSideRenderedContent.js

@@ -65,8 +65,9 @@ const NewHydrate = (0, mobx_react_1.observer)(function ServerSideRenderedContent
             });
         };
     }, [html, theme, rest, hydrateFn, RenderingComponent]);
-    // eslint-disable-next-line react/no-danger
-    return react_1.default.createElement("div", { ref: ref, dangerouslySetInnerHTML: { __html: html } });
+    return (react_1.default.createElement("div", { "data-testid": "hydrationContainer", ref: ref, 
+        // eslint-disable-next-line react/no-danger
+        dangerouslySetInnerHTML: { __html: html } }));
 });
 const OldHydrate = (0, mobx_react_1.observer)(function ({ theme, html, RenderingComponent, ...rest }) {
     const ref = (0, react_1.useRef)(null);

package/rpc/BaseRpcDriver.d.ts

@@ -3,8 +3,8 @@ import { AnyConfigurationModel } from '../configuration';
 export interface WorkerHandle {
     status?: string;
     error?: Error;
-    on?: (channel: string, callback: (message: string) => void) => void;
-    off?: (channel: string, callback: (message: string) => void) => void;
+    on?: (channel: string, callback: (message: unknown) => void) => void;
+    off?: (channel: string, callback: (message: unknown) => void) => void;
     destroy(): void;
     call(functionName: string, args?: unknown, options?: {
         statusCallback?(message: string): void;
@@ -38,7 +38,7 @@ export default abstract class BaseRpcDriver {
     getWorkerPool(): LazyWorker[];
     getWorker(sessionId: string): Promise<WorkerHandle>;
     call(pluginManager: PluginManager, sessionId: string, functionName: string, args: {
-        statusCallback?: (message: string) => void;
+        statusCallback?: (message: unknown) => void;
     }, options?: {}): Promise<unknown>;
 }
 export {};

package/rpc/WebWorkerRpcDriver.d.ts

@@ -1,4 +1,3 @@
-/// <reference path="../../rpc/declaration.d.ts" />
 import Rpc from 'librpc-web-mod';
 import BaseRpcDriver, { RpcDriverConstructorArgs } from './BaseRpcDriver';
 import { PluginDefinition } from '../PluginLoader';
@@ -6,12 +5,12 @@ interface WebWorkerRpcDriverConstructorArgs extends RpcDriverConstructorArgs {
     makeWorkerInstance: () => Worker;
 }
 interface Options {
-    statusCallback?: (arg0: string) => void;
+    statusCallback?: (arg0: unknown) => void;
     rpcDriverClassName: string;
 }
 declare class WebWorkerHandle extends Rpc.Client {
     destroy(): void;
-    call(funcName: string, args: Record<string, unknown>, opts: Options): Promise<any>;
+    call(funcName: string, args: Record<string, unknown>, opts: Options): Promise<unknown>;
 }
 export default class WebWorkerRpcDriver extends BaseRpcDriver {
     workerBootConfiguration: {

package/rpc/WebWorkerRpcDriver.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
 const serialize_error_1 = require("serialize-error");
+const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
 // locals
 const nanoid_1 = require("../util/nanoid");
 const BaseRpcDriver_1 = __importDefault(require("./BaseRpcDriver"));

package/rpc/methods/CoreRender.d.ts

@@ -9,6 +9,6 @@ export default class CoreRender extends RpcMethodType {
     serializeArguments(args: RenderArgs, rpcDriver: string): Promise<import("../../pluggableElementTypes/renderers/ServerSideRendererType").RenderArgsSerialized | RenderArgs>;
     execute(args: RenderArgsSerialized & {
         signal?: RemoteAbortSignal;
-    }, rpcDriver: string): Promise<ResultsSerialized | RenderResults>;
+    }, rpcDriver: string): Promise<RenderResults | ResultsSerialized>;
     deserializeReturn(serializedReturn: RenderResults | ResultsSerialized, args: RenderArgs, rpcDriver: string): Promise<unknown>;
 }