@jbrowse/core 3.2.0 → 3.4.0

package/TextSearch/TextSearchManager.d.ts

@@ -20,7 +20,13 @@ export default class TextSearchManager {
             [x: string]: any;
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
-    getAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): AnyConfigurationModel[];
+    getAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
+    } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     getTrackAdaptersWithAssembly(assemblyName: string, confs: AnyConfigurationModel[]): ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -29,5 +35,14 @@ export default class TextSearchManager {
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("../configuration").AnyConfigurationSchemaType>)[];
     search(args: BaseTextSearchArgs, searchScope: SearchScope, rankFn: (results: BaseResult[]) => BaseResult[]): Promise<BaseResult[]>;
-    sortResults(results: BaseResult[], rankFn: (results: BaseResult[]) => BaseResult[]): BaseResult[];
+    search2({ args, searchScope, rankFn, }: {
+        args: BaseTextSearchArgs;
+        searchScope: SearchScope;
+        rankFn: (results: BaseResult[]) => BaseResult[];
+    }): Promise<BaseResult[]>;
+    sortResults2({ results, rankFn, args, }: {
+        results: BaseResult[];
+        args: BaseTextSearchArgs;
+        rankFn: (results: BaseResult[]) => BaseResult[];
+    }): BaseResult[];
 }

package/TextSearch/TextSearchManager.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const ufuzzy_1 = __importDefault(require("@leeoniya/ufuzzy"));
 const configuration_1 = require("../configuration");
 const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
 class TextSearchManager {
@@ -54,12 +55,31 @@ class TextSearchManager {
             .map(conf => conf.textSearching.textSearchAdapter);
     }
     async search(args, searchScope, rankFn) {
+        return this.search2({ args, searchScope, rankFn });
+    }
+    async search2({ args, searchScope, rankFn, }) {
         const adapters = await this.loadTextSearchAdapters(searchScope);
         const results = await Promise.all(adapters.map(a => a.searchIndex(args)));
-        return this.sortResults(results.flat(), rankFn);
+        return this.sortResults2({
+            args,
+            results: results.flat(),
+            rankFn,
+        });
     }
-    sortResults(results, rankFn) {
-        return rankFn(results.sort((a, b) => -b.getLabel().localeCompare(a.getLabel()))).sort((r1, r2) => r1.getScore() - r2.getScore());
+    sortResults2({ results, rankFn, args, }) {
+        const uf = new ufuzzy_1.default({});
+        const haystack = results.map(r => r.getDisplayString());
+        const needle = args.queryString;
+        const idxs = uf.filter(haystack, needle);
+        const res = [];
+        if (idxs != null && idxs.length > 0) {
+            const info = uf.info(idxs, haystack, needle);
+            const order = uf.sort(info, haystack, needle);
+            for (const element of order) {
+                res.push(results[info.idx[element]]);
+            }
+        }
+        return rankFn(res);
     }
 }
 exports.default = TextSearchManager;

package/assemblyManager/assemblyManager.js

@@ -86,7 +86,7 @@ function assemblyManagerFactory(conf, pm) {
             if (assembly) {
                 return assembly.isValidRefName(refName);
             }
-            throw new Error(`Failed to look up refName ${refName} on ${assemblyName} because assembly does not exist`);
+            throw new Error(`Failed to look up refName:${refName} on assemblyName:${assemblyName} (assembly does not exist)`);
         },
     }))
         .actions(self => ({

package/data_adapters/BaseAdapter/BaseAdapter.d.ts

@@ -2,7 +2,7 @@ import type PluginManager from '../../PluginManager';
 import type { AnyConfigurationModel } from '../../configuration';
 import type { AugmentedRegion as Region } from '../../util/types';
 import type { getSubAdapterType } from '../dataAdapterCache';
-export declare abstract class BaseAdapter {
+export declare class BaseAdapter {
     config: AnyConfigurationModel;
     getSubAdapter?: getSubAdapterType | undefined;
     pluginManager?: PluginManager | undefined;
@@ -10,5 +10,5 @@ export declare abstract class BaseAdapter {
     static capabilities: string[];
     constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
     getConf(arg: string | string[]): any;
-    abstract freeResources(region: Region): void;
+    freeResources(_region: Region): void;
 }

package/data_adapters/BaseAdapter/BaseAdapter.js

@@ -24,6 +24,7 @@ class BaseAdapter {
     getConf(arg) {
         return (0, configuration_1.readConfObject)(this.config, arg);
     }
+    freeResources(_region) { }
 }
 exports.BaseAdapter = BaseAdapter;
 BaseAdapter.capabilities = [];

package/data_adapters/CytobandAdapter/CytobandAdapter.d.ts

@@ -3,5 +3,4 @@ import { BaseAdapter } from '../BaseAdapter';
 import type { BaseOptions } from '../BaseAdapter/BaseOptions';
 export default class CytobandAdapter extends BaseAdapter {
     getData(opts?: BaseOptions): Promise<SimpleFeature[]>;
-    freeResources(): void;
 }

package/data_adapters/CytobandAdapter/CytobandAdapter.js

@@ -13,6 +13,7 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
         return text
             .split(/\n|\r\n|\r/)
             .filter(f => !!f.trim())
+            .filter(f => !f.startsWith('#'))
             .map((line, i) => {
             const [refName, start, end, name, type] = line.split('\t');
             return new util_1.SimpleFeature({
@@ -26,6 +27,5 @@ class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
             });
         });
     }
-    freeResources() { }
 }
 exports.default = CytobandAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "3.2.0",
+  "version": "3.4.0",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -31,12 +31,13 @@
   },
   "dependencies": {
     "@floating-ui/react": "^0.27.0",
-    "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/bgzf-filehandle": "^2.0.1",
-    "@gmod/http-range-fetcher": "^4.0.0",
-    "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
-    "@mui/x-data-grid": "^7.0.0",
+    "@gmod/abortable-promise-cache": "^3.0.1",
+    "@gmod/bgzf-filehandle": "^3.0.2",
+    "@gmod/http-range-fetcher": "^5.0.0",
+    "@leeoniya/ufuzzy": "^1.0.18",
+    "@mui/icons-material": "^7.0.0",
+    "@mui/material": "^7.0.0",
+    "@mui/x-data-grid": "^8.0.0",
     "canvas-sequencer": "^3.1.0",
     "canvas2svg": "^1.0.16",
     "colord": "^2.9.3",
@@ -46,7 +47,7 @@
     "dompurify": "^3.2.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle2": "^1.0.0",
+    "generic-filehandle2": "^2.0.1",
     "jexl": "^2.3.0",
     "librpc-web-mod": "^1.1.5",
     "load-script": "^2.0.0",
@@ -69,5 +70,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "c750e3f56706a490c19ba75abd807fec5e38aebf"
+  "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
 }

package/pluggableElementTypes/models/baseTrackConfig.js

@@ -86,17 +86,34 @@ function createBaseTrackConfig(pluginManager) {
             const snap = pluginManager.evaluateExtensionPoint('Core-preProcessTrackConfig', structuredClone(s2));
             const { displays = [] } = snap;
             if (snap.trackId !== 'placeholderId') {
-                const configDisplayTypes = new Set(displays.map(d => d.type));
-                for (const d of pluginManager.getTrackType(snap.type).displayTypes) {
-                    if (!configDisplayTypes.has(d.name)) {
-                        displays.push({
-                            displayId: `${snap.trackId}-${d.name}`,
-                            type: d.name,
-                        });
+                try {
+                    const configDisplayTypes = new Set(displays.map(d => d.type));
+                    for (const d of pluginManager.getTrackType(snap.type)
+                        .displayTypes) {
+                        if (!configDisplayTypes.has(d.name)) {
+                            displays.push({
+                                displayId: `${snap.trackId}-${d.name}`,
+                                type: d.name,
+                            });
+                        }
                     }
                 }
+                catch (e) {
+                    throw new Error(`Unknown track type "${snap.type}" in ${JSON.stringify(snap)}`, {
+                        cause: e,
+                    });
+                }
             }
-            return { ...snap, displays };
+            return {
+                ...snap,
+                displays: displays.map(d => {
+                    var _a;
+                    return ({
+                        ...d,
+                        displayId: (_a = d.displayId) !== null && _a !== void 0 ? _a : `${snap.trackId}-${d.type}`,
+                    });
+                }),
+            };
         },
         explicitIdentifier: 'trackId',
         explicitlyTyped: true,

package/pluggableElementTypes/renderers/CircularChordRendererType.js

@@ -14,22 +14,21 @@ class CircularChordRendererType extends FeatureRendererType_1.default {
     }
     deserializeResultsInClient(res, args) {
         const deserializedFeatures = new Map(res.features.map(f => util_1.SimpleFeature.fromJSON(f)).map(f => [f.id(), f]));
-        if (args.exportSVG) {
-            return {
+        return args.exportSVG
+            ? {
                 ...res,
                 features: deserializedFeatures,
                 blockKey: 'circularChord',
                 html: this.supportsSVG
                     ? res.html
                     : '<text y="12" fill="black">SVG export not supported for this track</text>',
+            }
+            : {
+                ...res,
+                features: deserializedFeatures,
+                blockKey: 'circularChord',
+                reactElement: ((0, jsx_runtime_1.jsx)(RpcRenderedSvgGroup_1.default, { ...args, ...res, features: deserializedFeatures, RenderingComponent: this.ReactComponent })),
             };
-        }
-        return {
-            ...res,
-            features: deserializedFeatures,
-            blockKey: 'circularChord',
-            reactElement: ((0, jsx_runtime_1.jsx)(RpcRenderedSvgGroup_1.default, { ...args, ...res, features: deserializedFeatures, RenderingComponent: this.ReactComponent })),
-        };
     }
 }
 exports.default = CircularChordRendererType;

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -72,8 +72,14 @@ class FeatureRendererType extends ServerSideRendererType_1.default {
     }
     async render(props) {
         const features = props.features || (await this.getFeatures(props));
-        const result = await super.render({ ...props, features });
-        return { ...result, features };
+        const result = await super.render({
+            ...props,
+            features,
+        });
+        return {
+            ...result,
+            features,
+        };
     }
 }
 exports.default = FeatureRendererType;

package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.d.ts

@@ -1,11 +1,9 @@
 import type { AnyReactComponentType, Feature } from '../../util';
 import type { ThemeOptions } from '@mui/material';
-interface Props {
+declare const RpcRenderedSvgGroup: (props: {
     html: string;
     features: Map<string, Feature>;
     theme: ThemeOptions;
-    displayModel?: any;
     RenderingComponent: AnyReactComponentType;
-}
-declare const RpcRenderedSvgGroup: (props: Props) => import("react/jsx-runtime").JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default RpcRenderedSvgGroup;

package/pluggableElementTypes/renderers/RpcRenderedSvgGroup.js

@@ -1,37 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const client_1 = require("react-dom/client");
-const ui_1 = require("../../ui");
-const util_1 = require("../../util");
 const RpcRenderedSvgGroup = (0, mobx_react_1.observer)(function RpcRenderedSvgGroup(props) {
-    const { html, theme, RenderingComponent, ...rest } = props;
-    const ref = (0, react_1.useRef)(null);
-    const rootRef = (0, react_1.useRef)(null);
-    (0, react_1.useEffect)(() => {
-        const renderTimeout = (0, util_1.rIC)(() => {
-            var _a;
-            if (!ref.current) {
-                return;
-            }
-            const jbrowseTheme = (0, ui_1.createJBrowseTheme)(theme);
-            rootRef.current =
-                (_a = rootRef.current) !== null && _a !== void 0 ? _a : (0, client_1.hydrateRoot)(ref.current, (0, jsx_runtime_1.jsx)(material_1.ThemeProvider, { theme: jbrowseTheme, children: (0, jsx_runtime_1.jsx)(RenderingComponent, { ...rest }) }));
-        });
-        return () => {
-            if (renderTimeout !== undefined) {
-                clearTimeout(renderTimeout);
-            }
-            const root = rootRef.current;
-            rootRef.current = null;
-            setTimeout(() => {
-                root === null || root === void 0 ? void 0 : root.unmount();
-            });
-        };
-    }, [RenderingComponent, theme, rest]);
-    return (0, jsx_runtime_1.jsx)("g", { ref: ref, dangerouslySetInnerHTML: { __html: html } });
+    const { html, RenderingComponent, ...rest } = props;
+    return (0, jsx_runtime_1.jsx)(RenderingComponent, { ...rest });
 });
 exports.default = RpcRenderedSvgGroup;

package/pluggableElementTypes/renderers/ServerSideRenderedContent.d.ts

@@ -2,5 +2,5 @@ import type { RenderArgs, ResultsSerialized } from './ServerSideRendererType';
 interface Props extends ResultsSerialized, RenderArgs {
     RenderingComponent: React.ComponentType<any>;
 }
-declare const ServerSideRenderedContent: ({ theme, html, RenderingComponent, ...rest }: Props) => import("react/jsx-runtime").JSX.Element;
+declare const ServerSideRenderedContent: ({ html, RenderingComponent, ...props }: Props) => import("react/jsx-runtime").JSX.Element;
 export default ServerSideRenderedContent;

package/pluggableElementTypes/renderers/ServerSideRenderedContent.js

@@ -1,36 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const styles_1 = require("@mui/material/styles");
 const mobx_react_1 = require("mobx-react");
-const client_1 = require("react-dom/client");
-const ui_1 = require("../../ui");
-const util_1 = require("../../util");
-const ServerSideRenderedContent = (0, mobx_react_1.observer)(function ServerSideRenderedContent({ theme, html, RenderingComponent, ...rest }) {
-    const ref = (0, react_1.useRef)(null);
-    const rootRef = (0, react_1.useRef)(null);
-    (0, react_1.useEffect)(() => {
-        const renderTimeout = (0, util_1.rIC)(() => {
-            var _a;
-            if (!ref.current) {
-                return;
-            }
-            const jbrowseTheme = (0, ui_1.createJBrowseTheme)(theme);
-            rootRef.current =
-                (_a = rootRef.current) !== null && _a !== void 0 ? _a : (0, client_1.hydrateRoot)(ref.current, (0, jsx_runtime_1.jsx)(styles_1.ThemeProvider, { theme: jbrowseTheme, children: (0, jsx_runtime_1.jsx)(RenderingComponent, { ...rest }) }));
-        });
-        return () => {
-            if (renderTimeout !== undefined) {
-                clearTimeout(renderTimeout);
-            }
-            const root = rootRef.current;
-            rootRef.current = null;
-            setTimeout(() => {
-                root === null || root === void 0 ? void 0 : root.unmount();
-            });
-        };
-    }, [theme, rest, RenderingComponent]);
-    return (0, jsx_runtime_1.jsx)("div", { ref: ref, dangerouslySetInnerHTML: { __html: html } });
+const ServerSideRenderedContent = (0, mobx_react_1.observer)(function ServerSideRenderedContent({ html, RenderingComponent, ...props }) {
+    return (0, jsx_runtime_1.jsx)(RenderingComponent, { ...props });
 });
 exports.default = ServerSideRenderedContent;

package/pluggableElementTypes/renderers/ServerSideRendererType.js

@@ -28,18 +28,17 @@ class ServerSideRenderer extends RendererType_1.default {
         };
     }
     deserializeResultsInClient(res, args) {
-        if (args.exportSVG) {
-            return {
+        return args.exportSVG
+            ? {
                 ...res,
                 html: this.supportsSVG
                     ? res.html
                     : '<text y="12" fill="black">SVG export not supported for this track</text>',
+            }
+            : {
+                ...res,
+                reactElement: ((0, jsx_runtime_1.jsx)(ServerSideRenderedContent_1.default, { ...args, ...res, RenderingComponent: this.ReactComponent })),
             };
-        }
-        return {
-            ...res,
-            reactElement: ((0, jsx_runtime_1.jsx)(ServerSideRenderedContent_1.default, { ...args, ...res, RenderingComponent: this.ReactComponent })),
-        };
     }
     deserializeArgsInWorker(args) {
         const deserialized = { ...args };