@jbrowse/plugin-data-management 2.2.1 → 2.3.0

package/dist/AddTrackWidget/components/AddTrackWidget.js

@@ -1,25 +1,48 @@
 "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 = __importDefault(require("react"));
+const react_1 = __importStar(require("react"));
 const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 const DefaultAddTrackWorkflow_1 = __importDefault(require("./DefaultAddTrackWorkflow"));
 const PasteConfigWorkflow_1 = __importDefault(require("./PasteConfigWorkflow"));
 function AddTrackSelector({ model }) {
-    const [val, setVal] = (0, util_1.useLocalStorage)('trackSelector-choice', 'Default');
+    const [val, setVal] = (0, react_1.useState)('Default add track workflow');
     const { pluginManager } = (0, util_1.getEnv)(model);
-    const widgets = pluginManager.getElementTypesInGroup('add track workflow');
+    const widgets = pluginManager.getAddTrackWorkflowElements();
     const ComponentMap = {
-        Default: DefaultAddTrackWorkflow_1.default,
+        'Default add track workflow': DefaultAddTrackWorkflow_1.default,
         'Add track JSON': PasteConfigWorkflow_1.default,
         ...Object.fromEntries(widgets.map(w => [w.name, w.ReactComponent])),
     };
     // make sure the selected value is in the list
-    const val2 = ComponentMap[val] ? val : 'Default';
+    const val2 = ComponentMap[val] ? val : 'Default add track workflow';
     const Component = ComponentMap[val2];
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.FormControl, null,

package/dist/AddTrackWidget/components/AddTrackWidget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddTrackWidget.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/AddTrackWidget.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAuC;AACvC,2CAAqC;AACrC,4CAA6E;AAC7E,6CAA2C;AAI3C,wFAA+D;AAC/D,gFAAuD;AAEvD,SAAS,gBAAgB,CAAC,EAAE,KAAK,EAA4B;IAC3D,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,GAAG,IAAA,gBAAQ,EAAC,4BAA4B,CAAC,CAAA;IAC5D,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,KAAK,CAAC,CAAA;IACvC,MAAM,OAAO,GAAG,aAAa,CAAC,2BAA2B,EAAE,CAAA;IAC3D,MAAM,YAAY,GAAG;QACnB,4BAA4B,EAAE,iCAAuB;QACrD,gBAAgB,EAAE,6BAAmB;QACrC,GAAG,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;KACX,CAAA;IAE1D,8CAA8C;IAC9C,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,4BAA4B,CAAA;IACnE,MAAM,SAAS,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;IACpC,OAAO,CACL;QACE,8BAAC,sBAAW;YACV,8BAAC,iBAAM,IAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,IAC/D,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAClC,8BAAC,mBAAQ,IAAC,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,IACvB,CAAC,CACO,CACZ,CAAC,CACK;YACT,8BAAC,yBAAc,qCAA4C,CAC/C;QAEd,yCAAM;QACN,8BAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACJ,CAAA;AACH,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,gBAAgB,CAAC,CAAA"}

package/dist/AddTrackWidget/components/ConfirmTrack.d.ts

@@ -1,7 +1,6 @@
 /// <reference types="react" />
 import { AddTrackModel } from '../model';
-declare function ConfirmTrack({ model }: {
+declare const _default: ({ model, }: {
     model: AddTrackModel;
-}): JSX.Element;
-declare const _default: typeof ConfirmTrack;
+}) => JSX.Element;
 export default _default;

package/dist/AddTrackWidget/components/ConfirmTrack.js

@@ -29,169 +29,36 @@ 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 configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-// icons
-const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
-const Add_1 = __importDefault(require("@mui/icons-material//Add"));
+const ui_1 = require("@jbrowse/core/ui");
+const TextIndexingConfig_1 = __importDefault(require("./TextIndexingConfig"));
+const TrackTypeSelector_1 = __importDefault(require("./TrackTypeSelector"));
+const TrackAdapterSelector_1 = __importDefault(require("./TrackAdapterSelector"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
     },
-    paper: {
-        display: 'flex',
-        flexDirection: 'column',
-        padding: theme.spacing(1),
-    },
-    spacer: {
-        height: theme.spacing(8),
-    },
-    card: {
-        marginTop: theme.spacing(1),
-    },
 }));
 function StatusMessage({ trackAdapter, trackType, }) {
-    var _a;
     const { classes } = useStyles();
-    return trackAdapter.type === 'SNPCoverageAdapter' ? (react_1.default.createElement(material_1.Typography, { className: classes.spacing },
+    const { type, subadapter } = trackAdapter;
+    return type === 'SNPCoverageAdapter' ? (react_1.default.createElement(material_1.Typography, { className: classes.spacing },
         "Selected ",
         react_1.default.createElement("code", null, trackType),
-        ". Using adapter",
-        ' ',
-        react_1.default.createElement("code", null, trackAdapter.type),
-        " with subadapter",
-        ' ',
-        react_1.default.createElement("code", null, (_a = trackAdapter.subadapter) === null || _a === void 0 ? void 0 : _a.type),
+        ". Using adapter ",
+        react_1.default.createElement("code", null, type),
+        " with subadapter ",
+        react_1.default.createElement("code", null, subadapter === null || subadapter === void 0 ? void 0 : subadapter.type),
         ". Please enter a track name and, if necessary, update the track type.")) : (react_1.default.createElement(material_1.Typography, { className: classes.spacing },
         "Using adapter ",
-        react_1.default.createElement("code", null, trackAdapter.type),
+        react_1.default.createElement("code", null, type),
         " and guessing track type",
         ' ',
         react_1.default.createElement("code", null, trackType),
         ". Please enter a track name and, if necessary, update the track type."));
 }
-/**
- * categorizeAdapters takes a list of adapters and sorts their menu item elements under an appropriate ListSubheader
- *  element. In this way, adapters that are from external plugins can have headers that differentiate them from the
- *  out-of-the-box plugins.
- * @param adaptersList - a list of adapters found in the PluginManager
- * @returns a series of JSX elements that are ListSubheaders followed by the adapters
- *   found under that subheader
- */
-function categorizeAdapters(adaptersList) {
-    let currentCategory = '';
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const items = [];
-    adaptersList.forEach(adapter => {
-        var _a, _b, _c, _d, _e, _f, _g, _h;
-        if ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) {
-            if (currentCategory !== ((_b = adapter.adapterMetadata) === null || _b === void 0 ? void 0 : _b.category)) {
-                currentCategory = (_c = adapter.adapterMetadata) === null || _c === void 0 ? void 0 : _c.category;
-                items.push(react_1.default.createElement(material_1.ListSubheader, { key: (_d = adapter.adapterMetadata) === null || _d === void 0 ? void 0 : _d.category, value: (_e = adapter.adapterMetadata) === null || _e === void 0 ? void 0 : _e.category }, (_f = adapter.adapterMetadata) === null || _f === void 0 ? void 0 : _f.category));
-            }
-            items.push(react_1.default.createElement(material_1.MenuItem, { key: adapter.name, value: adapter.name }, ((_g = adapter.adapterMetadata) === null || _g === void 0 ? void 0 : _g.displayName)
-                ? (_h = adapter.adapterMetadata) === null || _h === void 0 ? void 0 : _h.displayName
-                : adapter.name));
-        }
-    });
-    return items;
-}
-function getAdapterTypes(pluginManager) {
-    return pluginManager.getElementTypesInGroup('adapter');
-}
-function getTrackTypes(pluginManager) {
-    return pluginManager.getElementTypesInGroup('track');
-}
-const TextIndexingConfig = (0, mobx_react_1.observer)(({ model }) => {
-    const { classes } = useStyles();
-    const [value1, setValue1] = (0, react_1.useState)('');
-    const [value2, setValue2] = (0, react_1.useState)('');
-    const [attributes, setAttributes] = (0, react_1.useState)(['Name', 'ID']);
-    const [exclude, setExclude] = (0, react_1.useState)(['CDS', 'exon']);
-    const sections = [
-        {
-            label: 'Indexing attributes',
-            values: attributes,
-        },
-        {
-            label: 'Feature types to exclude',
-            values: exclude,
-        },
-    ];
-    (0, react_1.useEffect)(() => {
-        model.setTextIndexingConf({ attributes, exclude });
-    }, [model, attributes, exclude]);
-    return (react_1.default.createElement(material_1.Paper, { className: classes.paper },
-        react_1.default.createElement(material_1.InputLabel, null, "Indexing configuration"),
-        sections.map((section, index) => (react_1.default.createElement(material_1.Card, { raised: true, key: section.label, className: classes.card },
-            react_1.default.createElement(material_1.CardContent, null,
-                react_1.default.createElement(material_1.InputLabel, null, section.label),
-                react_1.default.createElement(material_1.List, { disablePadding: true },
-                    section.values.map((val, idx) => (react_1.default.createElement(material_1.ListItem, { key: idx, disableGutters: true },
-                        react_1.default.createElement(material_1.TextField, { value: val, InputProps: {
-                                endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                                    react_1.default.createElement(material_1.IconButton, { color: "secondary", onClick: () => {
-                                            const newAttr = section.values.filter((a, i) => {
-                                                return i !== idx;
-                                            });
-                                            index === 0
-                                                ? setAttributes(newAttr)
-                                                : setExclude(newAttr);
-                                        } },
-                                        react_1.default.createElement(Delete_1.default, null)))),
-                            } })))),
-                    react_1.default.createElement(material_1.ListItem, { disableGutters: true },
-                        react_1.default.createElement(material_1.TextField, { value: index === 0 ? value1 : value2, placeholder: "add new", onChange: event => {
-                                index === 0
-                                    ? setValue1(event.target.value)
-                                    : setValue2(event.target.value);
-                            }, InputProps: {
-                                endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                                    react_1.default.createElement(material_1.IconButton, { onClick: () => {
-                                            if (index === 0) {
-                                                const newAttr = attributes;
-                                                newAttr.push(value1);
-                                                setAttributes(newAttr);
-                                                setValue1('');
-                                            }
-                                            else {
-                                                const newFeat = exclude;
-                                                newFeat.push(value2);
-                                                setExclude(newFeat);
-                                                setValue2('');
-                                            }
-                                        }, disabled: index === 0 ? value1 === '' : value2 === '', color: "secondary", "data-testid": `stringArrayAdd-Feat` },
-                                        react_1.default.createElement(Add_1.default, null)))),
-                            } })))))))));
-});
-const TrackAdapterSelector = (0, mobx_react_1.observer)(({ model }) => {
-    const { classes } = useStyles();
-    const { trackAdapter } = model;
-    const { pluginManager } = (0, util_1.getEnv)(model);
-    const adapters = getAdapterTypes(pluginManager);
-    return (react_1.default.createElement(material_1.TextField, { className: classes.spacing, value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "adapterType", helperText: "Select an adapter type", select: true, fullWidth: true, onChange: event => model.setAdapterHint(event.target.value), SelectProps: {
-            // @ts-ignore
-            SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
-        } },
-        adapters
-            // Excludes any adapter with the 'adapterMetadata.hiddenFromGUI' property, and anything with the 'adapterMetadata.category' property
-            .filter(elt => {
-            var _a, _b;
-            return !((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI) &&
-                !((_b = elt.adapterMetadata) === null || _b === void 0 ? void 0 : _b.category);
-        })
-            .map(elt => {
-            var _a, _b;
-            return (react_1.default.createElement(material_1.MenuItem, { key: elt.name, value: elt.name }, ((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.displayName)
-                ? (_b = elt.adapterMetadata) === null || _b === void 0 ? void 0 : _b.displayName
-                : elt.name));
-        }),
-        // adapters with the 'adapterMetadata.category' property are categorized
-        // by the value of the property here
-        categorizeAdapters(adapters.filter(elt => { var _a; return !((_a = elt.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI); }))));
-});
 function UnknownAdapterPrompt({ model }) {
     const { classes } = useStyles();
     return (react_1.default.createElement(react_1.default.Fragment, null,
@@ -205,34 +72,18 @@ function UnknownAdapterPrompt({ model }) {
             react_1.default.createElement(material_1.Link, { href: "https://github.com/GMOD/jbrowse-components/issues/new", target: "_blank", rel: "noopener noreferrer" }, "file an issue"),
             ' ',
             "and add a feature request for this data type."),
-        react_1.default.createElement(TrackAdapterSelector, { model: model })));
+        react_1.default.createElement(TrackAdapterSelector_1.default, { model: model })));
 }
-const TrackTypeSelector = (0, mobx_react_1.observer)(({ model }) => {
-    const { classes } = useStyles();
-    const session = (0, util_1.getSession)(model);
-    const { trackType } = model;
-    const trackTypes = getTrackTypes((0, util_1.getEnv)(session).pluginManager);
-    return (react_1.default.createElement(material_1.TextField, { className: classes.spacing, value: trackType, label: "trackType", helperText: "Select a track type", select: true, fullWidth: true, onChange: event => {
-            model.setTrackType(event.target.value);
-        }, SelectProps: {
-            // @ts-ignore
-            SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
-        } }, trackTypes.map(({ name }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, name)))));
-});
-const TrackAssemblySelector = (0, mobx_react_1.observer)(({ model }) => {
-    const session = (0, util_1.getSession)(model);
-    const { assembly } = model;
-    return (react_1.default.createElement(material_1.TextField, { value: assembly, label: "assemblyName", helperText: "Assembly to which the track will be added", select: true, fullWidth: true, onChange: event => model.setAssembly(event.target.value), SelectProps: {
-            // @ts-ignore
-            SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
-        } }, session.assemblies
-        .map(conf => (0, configuration_1.readConfObject)(conf, 'name'))
-        .map(name => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, name)))));
-});
-function ConfirmTrack({ model }) {
+exports.default = (0, mobx_react_1.observer)(function ConfirmTrack({ model, }) {
     const { classes } = useStyles();
     const [check, setCheck] = (0, react_1.useState)(true);
+    const session = (0, util_1.getSession)(model);
     const { trackName, trackAdapter, trackType, warningMessage, adapterHint } = model;
+    (0, react_1.useEffect)(() => {
+        if (adapterHint === '' && trackAdapter) {
+            model.setAdapterHint(trackAdapter.type);
+        }
+    }, [adapterHint, trackAdapter, trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type, model]);
     if (model.unsupported) {
         return (react_1.default.createElement(material_1.Typography, { className: classes.spacing },
             "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can",
@@ -248,9 +99,6 @@ function ConfirmTrack({ model }) {
     if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === tracks_1.UNKNOWN) {
         return react_1.default.createElement(UnknownAdapterPrompt, { model: model });
     }
-    if (adapterHint === '' && trackAdapter) {
-        model.setAdapterHint(trackAdapter.type);
-    }
     if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
         return react_1.default.createElement(material_1.Typography, null, "Could not recognize this data type.");
     }
@@ -259,15 +107,20 @@ function ConfirmTrack({ model }) {
         trackAdapter ? (react_1.default.createElement(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType })) : null,
         warningMessage ? (react_1.default.createElement(material_1.Typography, { style: { color: 'orange' } }, warningMessage)) : null,
         react_1.default.createElement(material_1.TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => model.setTrackName(event.target.value), inputProps: { 'data-testid': 'trackNameInput' } }),
-        react_1.default.createElement(TrackAdapterSelector, { model: model }),
-        react_1.default.createElement(TrackTypeSelector, { model: model }),
-        react_1.default.createElement(TrackAssemblySelector, { model: model }),
+        react_1.default.createElement(TrackAdapterSelector_1.default, { model: model }),
+        react_1.default.createElement(TrackTypeSelector_1.default, { model: model }),
+        react_1.default.createElement(ui_1.AssemblySelector, { session: session, helperText: "Select assembly to add track to", selected: model.assembly, onChange: asm => model.setAssembly(asm), TextFieldProps: {
+                fullWidth: true,
+                SelectProps: {
+                    // @ts-ignore
+                    SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
+                },
+            } }),
         util_1.isElectron && supportedForIndexing && (react_1.default.createElement(material_1.FormControl, null,
             react_1.default.createElement(material_1.FormControlLabel, { label: 'Index track for text searching?', control: react_1.default.createElement(material_1.Checkbox, { checked: check, onChange: e => {
                         setCheck(e.target.checked);
                         model.setTextIndexTrack(e.target.checked);
                     } }) }))),
-        util_1.isElectron && check && supportedForIndexing ? (react_1.default.createElement(TextIndexingConfig, { model: model })) : null));
-}
-exports.default = (0, mobx_react_1.observer)(ConfirmTrack);
+        util_1.isElectron && check && supportedForIndexing ? (react_1.default.createElement(TextIndexingConfig_1.default, { model: model })) : null));
+});
 //# sourceMappingURL=ConfirmTrack.js.map

package/dist/AddTrackWidget/components/ConfirmTrack.js.map

@@ -1 +1 @@
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package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js.map

@@ -1 +1 @@
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package/dist/AddTrackWidget/components/TextIndexingConfig.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare const TextIndexingConfig: ({ model }: {
+    model: AddTrackModel;
+}) => JSX.Element;
+export default TextIndexingConfig;

package/dist/AddTrackWidget/components/TextIndexingConfig.js

@@ -0,0 +1,109 @@
+"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 mobx_react_1 = require("mobx-react");
+// icons
+const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
+const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    paper: {
+        display: 'flex',
+        flexDirection: 'column',
+        padding: theme.spacing(1),
+    },
+    card: {
+        marginTop: theme.spacing(1),
+    },
+}));
+const TextIndexingConfig = (0, mobx_react_1.observer)(({ model }) => {
+    const { classes } = useStyles();
+    const [value1, setValue1] = (0, react_1.useState)('');
+    const [value2, setValue2] = (0, react_1.useState)('');
+    const [attributes, setAttributes] = (0, react_1.useState)(['Name', 'ID']);
+    const [exclude, setExclude] = (0, react_1.useState)(['CDS', 'exon']);
+    const sections = [
+        {
+            label: 'Indexing attributes',
+            values: attributes,
+        },
+        {
+            label: 'Feature types to exclude',
+            values: exclude,
+        },
+    ];
+    (0, react_1.useEffect)(() => {
+        model.setTextIndexingConf({ attributes, exclude });
+    }, [model, attributes, exclude]);
+    return (react_1.default.createElement(material_1.Paper, { className: classes.paper },
+        react_1.default.createElement(material_1.InputLabel, null, "Indexing configuration"),
+        sections.map((section, index) => (react_1.default.createElement(material_1.Card, { raised: true, key: section.label, className: classes.card },
+            react_1.default.createElement(material_1.CardContent, null,
+                react_1.default.createElement(material_1.InputLabel, null, section.label),
+                react_1.default.createElement(material_1.List, { disablePadding: true },
+                    section.values.map((val, idx) => (react_1.default.createElement(material_1.ListItem, { key: idx, disableGutters: true },
+                        react_1.default.createElement(material_1.TextField, { value: val, InputProps: {
+                                endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
+                                    react_1.default.createElement(material_1.IconButton, { color: "secondary", onClick: () => {
+                                            const newAttr = section.values.filter((a, i) => {
+                                                return i !== idx;
+                                            });
+                                            index === 0
+                                                ? setAttributes(newAttr)
+                                                : setExclude(newAttr);
+                                        } },
+                                        react_1.default.createElement(Delete_1.default, null)))),
+                            } })))),
+                    react_1.default.createElement(material_1.ListItem, { disableGutters: true },
+                        react_1.default.createElement(material_1.TextField, { value: index === 0 ? value1 : value2, placeholder: "add new", onChange: event => {
+                                index === 0
+                                    ? setValue1(event.target.value)
+                                    : setValue2(event.target.value);
+                            }, InputProps: {
+                                endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
+                                    react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                                            if (index === 0) {
+                                                const newAttr = attributes;
+                                                newAttr.push(value1);
+                                                setAttributes(newAttr);
+                                                setValue1('');
+                                            }
+                                            else {
+                                                const newFeat = exclude;
+                                                newFeat.push(value2);
+                                                setExclude(newFeat);
+                                                setValue2('');
+                                            }
+                                        }, disabled: index === 0 ? value1 === '' : value2 === '', color: "secondary", "data-testid": `stringArrayAdd-Feat` },
+                                        react_1.default.createElement(Add_1.default, null)))),
+                            } })))))))));
+});
+exports.default = TextIndexingConfig;
+//# sourceMappingURL=TextIndexingConfig.js.map

package/dist/AddTrackWidget/components/TextIndexingConfig.js.map

@@ -0,0 +1 @@
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package/dist/AddTrackWidget/components/TrackAdapterSelector.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare const TrackAdapterSelector: ({ model }: {
+    model: AddTrackModel;
+}) => JSX.Element;
+export default TrackAdapterSelector;

package/dist/AddTrackWidget/components/TrackAdapterSelector.js

@@ -0,0 +1,50 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    spacing: {
+        marginBottom: theme.spacing(3),
+    },
+}));
+// collate adapters into a map with
+// key: category
+// value: array of adapters with that category
+function categorizeAdapters(adaptersList) {
+    const map = {};
+    adaptersList.forEach(adapter => {
+        var _a;
+        const key = ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) || 'Default';
+        if (!map[key]) {
+            map[key] = [];
+        }
+        map[key].push(adapter);
+    });
+    return map;
+}
+const TrackAdapterSelector = (0, mobx_react_1.observer)(({ model }) => {
+    const { classes } = useStyles();
+    const { trackAdapter } = model;
+    const { pluginManager } = (0, util_1.getEnv)(model);
+    return (react_1.default.createElement(material_1.TextField, { className: classes.spacing, value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "Adapter type", variant: "outlined", helperText: "Select an adapter type", select: true, fullWidth: true, onChange: event => model.setAdapterHint(event.target.value), SelectProps: {
+            // @ts-ignore
+            SelectDisplayProps: { 'data-testid': 'adapterTypeSelect' },
+        } }, Object.entries(categorizeAdapters(pluginManager
+        .getAdapterElements()
+        .filter(e => { var _a; return !((_a = e.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI); }))).map(([key, val]) => {
+        // returning array avoids needing to use a react fragment which
+        // Select/TextField sub-elements disagree with
+        return [
+            react_1.default.createElement(material_1.ListSubheader, null, key),
+            val.map(elt => (react_1.default.createElement(material_1.MenuItem, { key: elt.name, value: elt.name }, elt.displayName))),
+        ];
+    })));
+});
+exports.default = TrackAdapterSelector;
+//# sourceMappingURL=TrackAdapterSelector.js.map

package/dist/AddTrackWidget/components/TrackAdapterSelector.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"TrackAdapterSelector.js","sourceRoot":"","sources":["../../../src/AddTrackWidget/components/TrackAdapterSelector.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAkE;AAClE,uCAA0C;AAC1C,6CAA2C;AAC3C,2CAAqC;AAMrC,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,YAAY,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC/B;CACF,CAAC,CAAC,CAAA;AAEH,mCAAmC;AACnC,gBAAgB;AAChB,8CAA8C;AAC9C,SAAS,kBAAkB,CAAC,YAA2B;IACrD,MAAM,GAAG,GAAG,EAAsC,CAAA;IAClD,YAAY,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE;;QAC7B,MAAM,GAAG,GAAG,CAAA,MAAA,OAAO,CAAC,eAAe,0CAAE,QAAQ,KAAI,SAAS,CAAA;QAC1D,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE;YACb,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,CAAA;SACd;QACD,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;IACxB,CAAC,CAAC,CAAA;IACF,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,MAAM,oBAAoB,GAAG,IAAA,qBAAQ,EAAC,CAAC,EAAE,KAAK,EAA4B,EAAE,EAAE;IAC5E,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,EAAE,YAAY,EAAE,GAAG,KAAK,CAAA;IAC9B,MAAM,EAAE,aAAa,EAAE,GAAG,IAAA,aAAM,EAAC,KAAK,CAAC,CAAA;IACvC,OAAO,CACL,8BAAC,oBAAS,IACR,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,KAAK,EAAE,CAAA,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,IAAI,MAAK,SAAS,CAAC,CAAC,CAAC,YAAY,aAAZ,YAAY,uBAAZ,YAAY,CAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EACjE,KAAK,EAAC,cAAc,EACpB,OAAO,EAAC,UAAU,EAClB,UAAU,EAAC,wBAAwB,EACnC,MAAM,QACN,SAAS,QACT,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,EAC3D,WAAW,EAAE;YACX,aAAa;YACb,kBAAkB,EAAE,EAAE,aAAa,EAAE,mBAAmB,EAAE;SAC3D,IAEA,MAAM,CAAC,OAAO,CACb,kBAAkB,CAChB,aAAa;SACV,kBAAkB,EAAE;SACpB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,CAAC,CAAA,MAAA,CAAC,CAAC,eAAe,0CAAE,aAAa,CAAA,CAAA,EAAA,CAAC,CAClD,CACF,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE;QACnB,+DAA+D;QAC/D,8CAA8C;QAC9C,OAAO;YACL,8BAAC,wBAAa,QAAE,GAAG,CAAiB;YACpC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,CACb,8BAAC,mBAAQ,IAAC,GAAG,EAAE,GAAG,CAAC,IAAI,EAAE,KAAK,EAAE,GAAG,CAAC,IAAI,IACrC,GAAG,CAAC,WAAW,CACP,CACZ,CAAC;SACH,CAAA;IACH,CAAC,CAAC,CACQ,CACb,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,oBAAoB,CAAA"}

package/dist/AddTrackWidget/components/TrackTypeSelector.d.ts

@@ -0,0 +1,6 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare const TrackTypeSelector: ({ model }: {
+    model: AddTrackModel;
+}) => JSX.Element;
+export default TrackTypeSelector;

package/dist/AddTrackWidget/components/TrackTypeSelector.js

@@ -0,0 +1,27 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    spacing: {
+        marginBottom: theme.spacing(3),
+    },
+}));
+const TrackTypeSelector = (0, mobx_react_1.observer)(({ model }) => {
+    const { classes } = useStyles();
+    const { pluginManager } = (0, util_1.getEnv)(model);
+    const { trackType } = model;
+    const trackTypes = pluginManager.getTrackElements();
+    return (react_1.default.createElement(material_1.TextField, { className: classes.spacing, value: trackType, variant: "outlined", label: "Track type", helperText: "Select track type", select: true, fullWidth: true, onChange: event => model.setTrackType(event.target.value), SelectProps: {
+            // @ts-ignore
+            SelectDisplayProps: { 'data-testid': 'trackTypeSelect' },
+        } }, trackTypes.map(({ name, displayName }) => (react_1.default.createElement(material_1.MenuItem, { key: name, value: name }, displayName)))));
+});
+exports.default = TrackTypeSelector;
+//# sourceMappingURL=TrackTypeSelector.js.map

package/dist/AddTrackWidget/components/TrackTypeSelector.js.map

@@ -0,0 +1 @@
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