@jbrowse/core 2.15.3 → 2.16.0

package/BaseFeatureWidget/BaseFeatureDetail/index.js

@@ -7,7 +7,7 @@ exports.Attributes = exports.BaseAttributes = exports.BaseCoreDetails = void 0;
 exports.BaseCard = BaseCard;
 exports.FeatureDetails = FeatureDetails;
 const react_1 = __importDefault(require("react"));
-const react_error_boundary_1 = require("react-error-boundary");
+const ErrorBoundary_1 = require("@jbrowse/core/ui/ErrorBoundary");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
@@ -120,7 +120,7 @@ function FeatureDetails(props) {
         react_1.default.createElement(material_1.Divider, null),
         react_1.default.createElement(material_1.Typography, null, "Attributes"),
         react_1.default.createElement(Attributes_1.default, { attributes: feature, ...props, omit: omit, omitSingleLevel: coreDetails }),
-        react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { FallbackComponent: e => react_1.default.createElement(ui_1.ErrorMessage, { error: e.error }) },
+        react_1.default.createElement(ErrorBoundary_1.ErrorBoundary, { FallbackComponent: e => react_1.default.createElement(ui_1.ErrorMessage, { error: e.error }) },
             react_1.default.createElement(SequenceFeatureDetails_1.default, { ...props })),
         ExtraPanel ? (react_1.default.createElement(react_1.default.Fragment, null,
             react_1.default.createElement(material_1.Divider, null),

package/PluginManager.d.ts

@@ -106,6 +106,7 @@ export default class PluginManager {
     addElementType(groupName: PluggableElementTypeGroup, creationCallback: (pluginManager: PluginManager) => PluggableElementType): this;
     getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase | undefined;
     getElementTypesInGroup(groupName: PluggableElementTypeGroup): PluggableElementBase[];
+    getViewElements(): ViewType[];
     getTrackElements(): TrackType[];
     getConnectionElements(): ConnectionType[];
     getAddTrackWorkflowElements(): AddTrackWorkflowType[];

package/PluginManager.js

@@ -242,6 +242,9 @@ class PluginManager {
     getElementTypesInGroup(groupName) {
         return this.getElementTypeRecord(groupName).all();
     }
+    getViewElements() {
+        return this.getElementTypesInGroup('view');
+    }
     getTrackElements() {
         return this.getElementTypesInGroup('track');
     }

package/assemblyManager/assemblyManager.d.ts

@@ -572,12 +572,5 @@ declare function assemblyManagerFactory(conf: IAnyType, pm: PluginManager): impo
      * used as a reference. snapshots cannot be used
      */
     addAssembly(configuration: any): void;
-    /**
-     * #action
-     * private: you would generally want to add to manipulate
-     * jbrowse.assemblies, session.sessionAssemblies, or
-     * session.temporaryAssemblies instead of using this directly
-     */
-    replaceAssembly(idx: number, configuration: any): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export default assemblyManagerFactory;

package/assemblyManager/assemblyManager.js

@@ -4,8 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("../util");
 const mobx_1 = require("mobx");
+// locals
+const util_1 = require("../util");
 const configuration_1 = require("../configuration");
 const assembly_1 = __importDefault(require("./assembly"));
 /**
@@ -130,16 +131,17 @@ function assemblyManagerFactory(conf, pm) {
         .actions(self => ({
         afterAttach() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.reaction)(() => self.assemblyList, assemblyConfs => {
-                self.assemblies.forEach(asm => {
+                for (const asm of self.assemblies) {
                     if (!asm.configuration) {
                         this.removeAssembly(asm);
                     }
-                });
-                assemblyConfs.forEach(conf => {
-                    if (!self.assemblies.some(a => a.name === (0, configuration_1.readConfObject)(conf, 'name'))) {
+                }
+                for (const conf of assemblyConfs) {
+                    const name = (0, configuration_1.readConfObject)(conf, 'name');
+                    if (!self.assemblies.some(a => a.name === name)) {
                         this.addAssembly(conf);
                     }
-                });
+                }
             }, { fireImmediately: true, name: 'assemblyManagerAfterAttach' }));
         },
         /**
@@ -164,15 +166,6 @@ function assemblyManagerFactory(conf, pm) {
         addAssembly(configuration) {
             self.assemblies.push({ configuration });
         },
-        /**
-         * #action
-         * private: you would generally want to add to manipulate
-         * jbrowse.assemblies, session.sessionAssemblies, or
-         * session.temporaryAssemblies instead of using this directly
-         */
-        replaceAssembly(idx, configuration) {
-            self.assemblies[idx] = (0, mobx_state_tree_1.cast)({ configuration });
-        },
     }));
 }
 exports.default = assemblyManagerFactory;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.15.3",
+  "version": "2.16.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -54,7 +54,6 @@
     "load-script": "^2.0.0",
     "material-ui-popup-state": "^5.0.0",
     "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"
@@ -73,5 +72,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "c0f82fe7b210622dd462e702641cc6da01109c6e"
+  "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
 }

package/pluggableElementTypes/ViewType.d.ts

@@ -7,17 +7,22 @@ type BasicView = React.ComponentType<{
     session?: IAnyStateTreeNode;
 }>;
 type ViewComponentType = React.LazyExoticComponent<BasicView> | BasicView;
+interface ViewMetadata {
+    hiddenFromGUI?: boolean;
+}
 export default class ViewType extends PluggableElementBase {
     ReactComponent: ViewComponentType;
     stateModel: IAnyModelType;
     displayTypes: DisplayType[];
+    viewMetadata: ViewMetadata;
     extendedName?: string;
     constructor(stuff: {
         name: string;
         displayName?: string;
-        ReactComponent: ViewComponentType;
         stateModel: IAnyModelType;
         extendedName?: string;
+        viewMetadata?: ViewMetadata;
+        ReactComponent: ViewComponentType;
     });
     addDisplayType(display: DisplayType): void;
 }

package/pluggableElementTypes/ViewType.js

@@ -8,7 +8,9 @@ class ViewType extends PluggableElementBase_1.default {
     constructor(stuff) {
         super(stuff);
         this.displayTypes = [];
+        this.viewMetadata = {};
         this.ReactComponent = stuff.ReactComponent;
+        this.viewMetadata = stuff.viewMetadata || {};
         this.stateModel = stuff.stateModel;
         this.extendedName = stuff.extendedName;
     }

package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.js

@@ -72,7 +72,6 @@ const OldHydrate = (0, mobx_react_1.observer)(function OldHydrate(props) {
         function doHydrate() {
             if (domNode && html) {
                 if (domNode.innerHTML) {
-                    // eslint-disable-next-line @typescript-eslint/no-deprecated
                     (0, react_dom_1.unmountComponentAtNode)(domNode);
                 }
                 // setting outline:none fixes react "focusable" element issue. see
@@ -83,7 +82,6 @@ const OldHydrate = (0, mobx_react_1.observer)(function OldHydrate(props) {
                 // hydration for when we have some free time. helps keep the
                 // framerate up.
                 (0, util_1.rIC)(() => {
-                    // eslint-disable-next-line @typescript-eslint/no-deprecated
                     (0, react_dom_1.hydrate)(react_1.default.createElement(RenderingComponent, { ...props }), domNode);
                 });
             }
@@ -91,7 +89,6 @@ const OldHydrate = (0, mobx_react_1.observer)(function OldHydrate(props) {
         doHydrate();
         return () => {
             if (domNode) {
-                // eslint-disable-next-line @typescript-eslint/no-deprecated
                 (0, react_dom_1.unmountComponentAtNode)(domNode);
             }
         };

package/pluggableElementTypes/renderers/ServerSideRenderedContent.js

@@ -75,11 +75,9 @@ const OldHydrate = (0, mobx_react_1.observer)(function ({ theme, html, Rendering
         const domNode = ref.current;
         function doHydrate() {
             if (domNode) {
-                // eslint-disable-next-line @typescript-eslint/no-deprecated
                 (0, react_dom_1.unmountComponentAtNode)(domNode);
                 domNode.innerHTML = html;
                 (0, util_1.rIC)(() => {
-                    // eslint-disable-next-line @typescript-eslint/no-deprecated
                     (0, react_dom_1.hydrate)(react_1.default.createElement(styles_1.ThemeProvider, { theme: jbrowseTheme },
                         react_1.default.createElement(RenderingComponent, { ...rest })), domNode);
                 });
@@ -88,7 +86,6 @@ const OldHydrate = (0, mobx_react_1.observer)(function ({ theme, html, Rendering
         doHydrate();
         return () => {
             if (domNode) {
-                // eslint-disable-next-line @typescript-eslint/no-deprecated
                 (0, react_dom_1.unmountComponentAtNode)(domNode);
             }
         };

package/rpc/BaseRpcDriver.js

@@ -5,7 +5,7 @@ const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("../util");
 const remoteAbortSignals_1 = require("./remoteAbortSignals");
 const configuration_1 = require("../configuration");
-function isClonable(thing) {
+function isCloneable(thing) {
     return !(typeof thing === 'function') && !(thing instanceof Error);
 }
 // watches the given worker object, returns a promise that will be rejected if
@@ -64,11 +64,11 @@ class BaseRpcDriver {
         this.workerCheckFrequency = 5000;
         this.config = args.config;
     }
-    // filter the given object and just remove any non-clonable things from it
+    // filter the given object and just remove any non-cloneable things from it
     filterArgs(thing, sessionId) {
         if (Array.isArray(thing)) {
             return thing
-                .filter(thing => isClonable(thing))
+                .filter(thing => isCloneable(thing))
                 .map(t => this.filterArgs(t, sessionId));
         }
         if (typeof thing === 'object' && thing !== null) {
@@ -85,7 +85,7 @@ class BaseRpcDriver {
                 return thing;
             }
             return Object.fromEntries(Object.entries(thing)
-                .filter(e => isClonable(e[1]))
+                .filter(e => isCloneable(e[1]))
                 .map(([k, v]) => [k, this.filterArgs(v, sessionId)]));
         }
         return thing;