@jbrowse/core 2.4.2 → 2.6.0

package/BaseFeatureWidget/SequenceFeatureDetails/hooks.js

@@ -0,0 +1,73 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.useFeatureSequence = void 0;
+const react_1 = require("react");
+const util_1 = require("../../util");
+const configuration_1 = require("../../configuration");
+const BPLIMIT = 500000;
+function useFeatureSequence(model, feature, upDownBp, forceLoad) {
+    const [sequence, setSequence] = (0, react_1.useState)();
+    const [error, setError] = (0, react_1.useState)();
+    (0, react_1.useEffect)(() => {
+        var _a;
+        let finished = false;
+        if (!model) {
+            return () => { };
+        }
+        const { assemblyManager, rpcManager } = (0, util_1.getSession)(model);
+        const [assemblyName] = ((_a = model.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        async function fetchSeq(start, end, refName) {
+            const assembly = await assemblyManager.waitForAssembly(assemblyName);
+            if (!assembly) {
+                throw new Error('assembly not found');
+            }
+            const sessionId = 'getSequence';
+            const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
+                adapterConfig: (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']),
+                sessionId,
+                regions: [
+                    {
+                        start,
+                        end,
+                        refName: assembly.getCanonicalRefName(refName),
+                        assemblyName,
+                    },
+                ],
+            });
+            const [feat] = feats;
+            return (feat === null || feat === void 0 ? void 0 : feat.get('seq')) || '';
+        }
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                setError(undefined);
+                const { start, end, refName } = feature;
+                if (!forceLoad && end - start > BPLIMIT) {
+                    setSequence({
+                        error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
+                    });
+                }
+                else {
+                    const b = start - upDownBp;
+                    const e = end + upDownBp;
+                    const seq = await fetchSeq(start, end, refName);
+                    const up = await fetchSeq(Math.max(0, b), start, refName);
+                    const down = await fetchSeq(end, e, refName);
+                    if (!finished) {
+                        setSequence({ seq, upstream: up, downstream: down });
+                    }
+                }
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+        return () => {
+            finished = true;
+        };
+    }, [feature, model, upDownBp, forceLoad]);
+    return { sequence, error };
+}
+exports.useFeatureSequence = useFeatureSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/index.d.ts

@@ -0,0 +1,3 @@
+import React from 'react';
+import { BaseProps } from './../types';
+export default function SequenceFeaturePanel({ model, feature }: BaseProps): React.JSX.Element | null;

package/BaseFeatureWidget/SequenceFeatureDetails/index.js

@@ -0,0 +1,68 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const ui_1 = require("../../ui");
+// icons
+const Help_1 = __importDefault(require("@mui/icons-material/Help"));
+// lazies
+const HelpDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceHelpDialog'))));
+const SequenceFeatureDetails = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SequenceFeatureDetails'))));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    formControl: {
+        margin: 0,
+    },
+    container: {
+        marginTop: theme.spacing(4),
+        marginBottom: theme.spacing(4),
+    },
+}));
+// display the stitched-together sequence of a gene's CDS, cDNA, or protein
+// sequence. this is a best effort and weird genomic phenomena could lead these
+// to not be 100% accurate
+function SequenceFeaturePanel({ model, feature }) {
+    const { classes } = useStyles();
+    const [shown, setShown] = (0, react_1.useState)(false);
+    const [helpShown, setHelpShown] = (0, react_1.useState)(false);
+    return !model ? null : (react_1.default.createElement("div", { className: classes.container },
+        react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => setShown(!shown) }, shown ? 'Hide feature sequence' : 'Show feature sequence'),
+        react_1.default.createElement(material_1.FormControl, { className: classes.formControl },
+            react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpShown(true) },
+                react_1.default.createElement(Help_1.default, null))),
+        shown ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement(ui_1.LoadingEllipses, null) },
+            react_1.default.createElement(SequenceFeatureDetails
+            /* eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion */
+            , { 
+                /* eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion */
+                key: feature.uniqueId, model: model, feature: feature }))) : null,
+        helpShown ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
+            react_1.default.createElement(HelpDlg, { handleClose: () => setHelpShown(false) }))) : null));
+}
+exports.default = SequenceFeaturePanel;

package/BaseFeatureWidget/{test_data → SequenceFeatureDetails/test_data}/DLGAP3.d.ts

@@ -1,20 +1,20 @@
 declare namespace _default {
-    const source: string;
-    const type: string;
-    const start: number;
-    const end: number;
-    const strand: number;
-    const phase: number;
-    const refName: string;
-    const id: string;
-    const dbxref: string[];
-    const name: string;
-    const description: string;
-    const gbkey: string;
-    const gene: string;
-    const gene_biotype: string;
-    const gene_synonym: string[];
-    const subfeatures: {
+    let source: string;
+    let type: string;
+    let start: number;
+    let end: number;
+    let strand: number;
+    let phase: number;
+    let refName: string;
+    let id: string;
+    let dbxref: string[];
+    let name: string;
+    let description: string;
+    let gbkey: string;
+    let gene: string;
+    let gene_biotype: string;
+    let gene_synonym: string[];
+    let subfeatures: {
         source: string;
         type: string;
         start: number;
@@ -75,6 +75,6 @@ declare namespace _default {
         uniqueId: string;
         parentId: string;
     }[];
-    const uniqueId: string;
+    let uniqueId: string;
 }
 export default _default;

package/BaseFeatureWidget/{test_data → SequenceFeatureDetails/test_data}/NCDN.d.ts

@@ -1,19 +1,19 @@
 declare namespace _default {
-    const source: string;
-    const type: string;
-    const start: number;
-    const end: number;
-    const strand: number;
-    const phase: number;
-    const refName: string;
-    const id: string;
-    const dbxref: string[];
-    const name: string;
-    const description: string;
-    const gbkey: string;
-    const gene: string;
-    const gene_biotype: string;
-    const subfeatures: ({
+    let source: string;
+    let type: string;
+    let start: number;
+    let end: number;
+    let strand: number;
+    let phase: number;
+    let refName: string;
+    let id: string;
+    let dbxref: string[];
+    let name: string;
+    let description: string;
+    let gbkey: string;
+    let gene: string;
+    let gene_biotype: string;
+    let subfeatures: ({
         source: string;
         type: string;
         start: number;
@@ -136,6 +136,6 @@ declare namespace _default {
         parentId: string;
         tag?: undefined;
     })[];
-    const uniqueId: string;
+    let uniqueId: string;
 }
 export default _default;

package/BaseFeatureWidget/SequenceFeatureDetails/util.d.ts

@@ -0,0 +1,6 @@
+export declare const intronColor: undefined;
+export declare const utrColor = "rgb(200,240,240)";
+export declare const proteinColor = "rgb(220,160,220)";
+export declare const cdsColor = "rgb(220,220,180)";
+export declare const updownstreamColor = "rgba(250,200,200)";
+export declare const genomeColor = "rgb(200,280,200)";

package/BaseFeatureWidget/SequenceFeatureDetails/util.js

@@ -0,0 +1,11 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.genomeColor = exports.updownstreamColor = exports.cdsColor = exports.proteinColor = exports.utrColor = exports.intronColor = void 0;
+// note that these are currently put into the style section instead of being
+// defined in classes to aid copy and paste to an external document e.g. word
+exports.intronColor = undefined;
+exports.utrColor = 'rgb(200,240,240)';
+exports.proteinColor = 'rgb(220,160,220)';
+exports.cdsColor = 'rgb(220,220,180)';
+exports.updownstreamColor = 'rgba(250,200,200)';
+exports.genomeColor = 'rgb(200,280,200)';

package/BaseFeatureWidget/index.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from '../PluginManager';
-declare const configSchema: import("../configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("../configuration/configurationSchema").ConfigurationSchemaType<{}, import("../configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -11,10 +11,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string, trackId?: string): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{

package/BaseFeatureWidget/index.js

@@ -36,6 +36,9 @@ function stateModelFactory(pluginManager) {
         trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
         trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
     })
+        .volatile(() => ({
+        error: undefined,
+    }))
         .actions(self => ({
         setFeatureData(featureData) {
             self.unformattedFeatureData = featureData;
@@ -50,30 +53,39 @@ function stateModelFactory(pluginManager) {
             self.trackId = trackId;
             self.trackType = type;
         },
+        setError(e) {
+            self.error = e;
+        },
     }))
         .actions(self => ({
         afterCreate() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 var _a, _b;
-                self.setExtra((_a = self.track) === null || _a === void 0 ? void 0 : _a.type, (_b = self.track) === null || _b === void 0 ? void 0 : _b.configuration.trackId);
-                const { unformattedFeatureData, track } = self;
-                const session = (0, util_1.getSession)(self);
-                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);
-                        const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
-                        formatSubfeatures(feature, depth, sub => {
-                            // eslint-disable-next-line no-underscore-dangle
-                            sub.__jbrowsefmt = combine('subfeatures', sub);
+                try {
+                    self.setExtra((_a = self.track) === null || _a === void 0 ? void 0 : _a.type, (_b = self.track) === null || _b === void 0 ? void 0 : _b.configuration.trackId);
+                    const { unformattedFeatureData, track } = self;
+                    const session = (0, util_1.getSession)(self);
+                    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);
+                            const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
+                            formatSubfeatures(feature, depth, sub => {
+                                // eslint-disable-next-line no-underscore-dangle
+                                sub.__jbrowsefmt = combine('subfeatures', sub);
+                            });
+                        }
+                        self.setFormattedData(feature);
                     }
-                    self.setFormattedData(feature);
+                }
+                catch (e) {
+                    console.error(e);
+                    self.setError(e);
                 }
             }));
         },

package/BaseFeatureWidget/types.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
 import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { SimpleFeatureSerializedNoId } from '../util/simpleFeature';
+import { SimpleFeatureSerialized } from '../util/simpleFeature';
 import { AbstractViewModel } from '../util';
 export interface BaseProps extends BaseCardProps {
-    feature: SimpleFeatureSerializedNoId;
+    feature: SimpleFeatureSerialized;
     formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
     model?: IAnyStateTreeNode & {

package/BaseFeatureWidget/util.js

@@ -24,10 +24,15 @@ function revlist(list, seqlen) {
         .sort((a, b) => a.start - b.start);
 }
 exports.revlist = revlist;
-// calculates UTRs using impliedUTRs logic
 function calculateUTRs(cds, exons) {
-    const firstCds = cds[0];
-    const lastCds = cds[cds.length - 1];
+    // checking length ensures the .at below are valid
+    if (!cds.length) {
+        return [];
+    }
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const firstCds = cds.at(0);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const lastCds = cds.at(-1);
     const firstCdsIdx = exons.findIndex(exon => exon.end >= firstCds.start && exon.start <= firstCds.start);
     const lastCdsIdx = exons.findIndex(exon => exon.end >= lastCds.end && exon.start <= lastCds.end);
     const lastCdsExon = exons[lastCdsIdx];
@@ -45,8 +50,13 @@ function calculateUTRs(cds, exons) {
 exports.calculateUTRs = calculateUTRs;
 // calculates UTRs using impliedUTRs logic, but there are no exon subfeatures
 function calculateUTRs2(cds, parentFeat) {
-    const firstCds = cds[0];
-    const lastCds = cds[cds.length - 1];
+    if (!cds.length) {
+        return [];
+    }
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const firstCds = cds.at(0);
+    // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+    const lastCds = cds.at(-1);
     const fiveUTRs = [{ start: parentFeat.start, end: firstCds.start }].map(elt => ({ ...elt, type: 'five_prime_UTR' }));
     const threeUTRs = [{ start: lastCds.end, end: parentFeat.end }].map(elt => ({
         ...elt,

package/Plugin.d.ts

@@ -1,5 +1,5 @@
 import PluginManager from './PluginManager';
-import { AnyConfigurationSchemaType } from './configuration/configurationSchema';
+import { AnyConfigurationSchemaType } from './configuration';
 /**
  * base class for a JBrowse plugin
  */

package/PluginLoader.js

@@ -25,6 +25,20 @@ function isCJSPluginDefinition(def) {
     return def.cjsUrl !== undefined;
 }
 exports.isCJSPluginDefinition = isCJSPluginDefinition;
+function pluginDescriptionString(pluginDefinition) {
+    var _a;
+    if (isUMDPluginDefinition(pluginDefinition)) {
+        return `UMD plugin ${pluginDefinition.name}`;
+    }
+    if (isESMPluginDefinition(pluginDefinition)) {
+        return `ESM plugin ${pluginDefinition.esmUrl ||
+            ((_a = pluginDefinition.esmLoc) === null || _a === void 0 ? void 0 : _a.uri)}`;
+    }
+    if (isCJSPluginDefinition(pluginDefinition)) {
+        return `CJS plugin ${pluginDefinition.cjsUrl}`;
+    }
+    return 'unknown plugin';
+}
 function isInWebWorker() {
     return Boolean('WorkerGlobalScope' in globalThis);
 }
@@ -115,6 +129,9 @@ class PluginLoader {
         else {
             throw new Error(`Could not determine plugin type: ${JSON.stringify(def)}`);
         }
+        if (!plugin.default) {
+            throw new Error(`${pluginDescriptionString(def)} does not have a default export, cannot load`);
+        }
         return plugin.default;
     }
     installGlobalReExports(target) {

package/PluginManager.d.ts

@@ -99,6 +99,7 @@ export default class PluginManager {
     getElementType(groupName: PluggableElementTypeGroup, typeName: string): PluggableElementBase;
     getElementTypesInGroup(groupName: PluggableElementTypeGroup): PluggableElementBase[];
     getTrackElements(): TrackType[];
+    getConnectionElements(): ConnectionType[];
     getAddTrackWorkflowElements(): AddTrackWorkflowType[];
     getRpcElements(): RpcMethodType[];
     getDisplayElements(): DisplayType[];
@@ -206,19 +207,20 @@ export default class PluginManager {
         '@jbrowse/core/util/mst-reflection': typeof import("./util/mst-reflection");
         '@jbrowse/core/util/rxjs': typeof import("./util/rxjs");
         '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': {
-            Attributes: (props: any) => JSX.Element;
-            FeatureDetails: (props: any) => JSX.Element;
-            BaseCard: (props: any) => JSX.Element;
+            Attributes: (props: any) => import("react").JSX.Element;
+            FeatureDetails: (props: any) => import("react").JSX.Element;
+            BaseCard: (props: any) => import("react").JSX.Element;
         };
         '@jbrowse/core/data_adapters/BaseAdapter': typeof import("./data_adapters/BaseAdapter");
         mobx: typeof import("mobx");
         'mobx-state-tree': typeof import("mobx-state-tree");
         react: typeof import("react");
+        'react/jsx-runtime': typeof import("react/jsx-runtime");
         'react-dom': typeof import("react-dom");
         'mobx-react': typeof import("mobx-react");
         '@mui/x-data-grid': {
             useGridApiContext: typeof import("@mui/x-data-grid").useGridApiContext;
-            useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/models/api/gridApiCommunity").GridApiCommunity>() => import("react").MutableRefObject<Api>;
+            useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon<any, any> = import("@mui/x-data-grid/internals").GridApiCommunity>() => import("react").MutableRefObject<Api>;
             useGridRootProps: () => import("@mui/x-data-grid/models/props/DataGridProps").DataGridProcessedProps<any>;
         };
         '@mui/material/utils': typeof import("@mui/material/utils");
@@ -243,7 +245,8 @@ export default class PluginManager {
             makeStyles: (args: any) => () => Record<string, string>;
         };
         '@mui/material': {
-            [k: string]: (props: any) => JSX.Element;
+            alpha: typeof import("@mui/system").alpha;
+            useTheme: typeof import("@mui/material").useTheme;
         };
         'prop-types': typeof import("prop-types");
         '@mui/material/styles': typeof import("@mui/material/styles");

package/PluginManager.js

@@ -236,6 +236,9 @@ class PluginManager {
     getTrackElements() {
         return this.getElementTypesInGroup('track');
     }
+    getConnectionElements() {
+        return this.getElementTypesInGroup('connection');
+    }
     getAddTrackWorkflowElements() {
         return this.getElementTypesInGroup('add track workflow');
     }

package/README.md

@@ -1,8 +1,6 @@
 # jbrowse-core
 
 [![NPM version](https://img.shields.io/npm/v/@jbrowse/core.svg?style=flat-square)](https://npmjs.org/package/@jbrowse/core)
-[![Build Status](https://img.shields.io/travis/GMOD/jbrowse-components/main.svg?style=flat-square)](https://travis-ci.org/GMOD/jbrowse-components)
-[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/jbrowse-components/main.svg?style=flat-square)](https://codecov.io/gh/GMOD/jbrowse-components/branch/main)
 
 Core JBrowse libraries used by most JBrowse plugins.
 

package/ReExports/list.js

@@ -9,6 +9,7 @@ exports.default = [
     'mobx',
     'mobx-state-tree',
     'react',
+    'react/jsx-runtime',
     'react-dom',
     'mobx-react',
     '@mui/x-data-grid',

package/ReExports/modules.d.ts

@@ -1,4 +1,5 @@
 import React from 'react';
+import * as ReactJSXRuntime from 'react/jsx-runtime';
 import * as ReactDom from 'react-dom';
 import * as mobx from 'mobx';
 import * as mst from 'mobx-state-tree';
@@ -123,19 +124,20 @@ declare const libs: {
     '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;
     '@jbrowse/core/util/rxjs': typeof rxjs;
     '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail': {
-        Attributes: (props: any) => JSX.Element;
-        FeatureDetails: (props: any) => JSX.Element;
-        BaseCard: (props: any) => JSX.Element;
+        Attributes: (props: any) => React.JSX.Element;
+        FeatureDetails: (props: any) => React.JSX.Element;
+        BaseCard: (props: any) => React.JSX.Element;
     };
     '@jbrowse/core/data_adapters/BaseAdapter': typeof BaseAdapterExports;
     mobx: typeof mobx;
     'mobx-state-tree': typeof mst;
     react: typeof React;
+    'react/jsx-runtime': typeof ReactJSXRuntime;
     'react-dom': typeof ReactDom;
     'mobx-react': typeof mxreact;
     '@mui/x-data-grid': {
         useGridApiContext: typeof useGridApiContext;
-        useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon = import("@mui/x-data-grid/models/api/gridApiCommunity").GridApiCommunity>() => React.MutableRefObject<Api>;
+        useGridApiRef: <Api extends import("@mui/x-data-grid").GridApiCommon<any, any> = import("@mui/x-data-grid/internals").GridApiCommunity>() => React.MutableRefObject<Api>;
         useGridRootProps: () => import("@mui/x-data-grid/models/props/DataGridProps").DataGridProcessedProps<any>;
     };
     '@mui/material/utils': typeof MUIUtils;
@@ -160,7 +162,8 @@ declare const libs: {
         makeStyles: (args: any) => () => Record<string, string>;
     };
     '@mui/material': {
-        [k: string]: (props: any) => JSX.Element;
+        alpha: typeof MUIStyles.alpha;
+        useTheme: typeof MUIStyles.useTheme;
     };
     'prop-types': typeof PropTypes;
     '@mui/material/styles': typeof MUIStyles;

package/ReExports/modules.js

@@ -28,6 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 // this is all the stuff that the pluginManager re-exports for plugins to use
 const react_1 = __importStar(require("react"));
+const ReactJSXRuntime = __importStar(require("react/jsx-runtime"));
 const ReactDom = __importStar(require("react-dom"));
 const mobx = __importStar(require("mobx"));
 const mst = __importStar(require("mobx-state-tree"));
@@ -208,9 +209,6 @@ const DataGridEntries = {
     GridArrowUpwardIcon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridArrowUpwardIcon,
     }))),
-    GridAutoSizer: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
-        default: module.GridAutoSizer,
-    }))),
     GridCellCheckboxForwardRef: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridCellCheckboxForwardRef,
     }))),
@@ -308,9 +306,6 @@ const DataGridEntries = {
     GridSaveAltIcon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridSaveAltIcon,
     }))),
-    GridScrollArea: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
-        default: module.GridScrollArea,
-    }))),
     GridSearchIcon: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('@mui/x-data-grid'))).then(module => ({
         default: module.GridSearchIcon,
     }))),
@@ -373,6 +368,7 @@ const libs = {
     mobx,
     'mobx-state-tree': mst,
     react: react_1.default,
+    'react/jsx-runtime': ReactJSXRuntime,
     'react-dom': ReactDom,
     'mobx-react': mxreact,
     '@mui/x-data-grid': {
@@ -395,7 +391,11 @@ const libs = {
             return () => useStyles().classes;
         },
     },
-    '@mui/material': LazyMUICore,
+    '@mui/material': {
+        ...LazyMUICore,
+        alpha: MUIStyles.alpha,
+        useTheme: MUIStyles.useTheme,
+    },
     'prop-types': prop_types_1.default,
     // end special case
     // material-ui subcomponents, should get rid of these

package/TextSearch/TextSearchManager.d.ts

@@ -1,15 +1,8 @@
 import BaseResult from './BaseResults';
 import PluginManager from '../PluginManager';
 import QuickLRU from '../util/QuickLRU';
-import { SearchType, BaseTextSearchAdapter } from '../data_adapters/BaseAdapter';
+import { BaseTextSearchAdapter, BaseTextSearchArgs } from '../data_adapters/BaseAdapter';
 import { AnyConfigurationModel } from '../configuration';
-export interface BaseArgs {
-    queryString: string;
-    searchType?: SearchType;
-    signal?: AbortSignal;
-    limit?: number;
-    pageNumber?: number;
-}
 export interface SearchScope {
     includeAggregateIndexes: boolean;
     assemblyName: string;
@@ -36,7 +29,7 @@ export default class TextSearchManager {
      * @param args - search options/arguments include: search query
      * limit of results to return, searchType...prefix | full | exact", etc.
      */
-    search(args: BaseArgs, searchScope: SearchScope, rankFn: (results: BaseResult[]) => BaseResult[]): Promise<BaseResult[]>;
+    search(args: BaseTextSearchArgs, searchScope: SearchScope, rankFn: (results: BaseResult[]) => BaseResult[]): Promise<BaseResult[]>;
     /**
      * Returns array of revelevant and sorted results
      * @param results - array of results from all text search adapters