@jbrowse/plugin-data-management 2.3.3 → 2.4.0

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.js

@@ -0,0 +1,60 @@
+import React, { useState } from 'react';
+import { IconButton, Typography } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import JBrowseMenu from '@jbrowse/core/ui/Menu';
+// icons
+import ArrowDropDownIcon from '@mui/icons-material/ArrowDropDown';
+import ArrowRightIcon from '@mui/icons-material/ArrowRight';
+import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
+// locals
+import { getAllChildren, treeToMap } from '../util';
+const useStyles = makeStyles()(theme => ({
+    contrastColor: {
+        color: theme.palette.tertiary.contrastText,
+    },
+    // margin:auto 0 to center text vertically
+    accordionText: {
+        margin: 'auto 0',
+        // width 100 so you can click anywhere on the category bar
+        width: '100%',
+    },
+}));
+export default function Category({ isOpen, setOpen, data, }) {
+    const { classes } = useStyles();
+    const [menuEl, setMenuEl] = useState(null);
+    const { name, model, id, tree, toggleCollapse } = data;
+    return (React.createElement("div", { className: classes.accordionText, onClick: () => {
+            if (!menuEl) {
+                toggleCollapse(id);
+                setOpen(!isOpen);
+            }
+        } },
+        React.createElement(Typography, null,
+            isOpen ? React.createElement(ArrowDropDownIcon, null) : React.createElement(ArrowRightIcon, null),
+            name,
+            React.createElement(IconButton, { onClick: event => {
+                    setMenuEl(event.currentTarget);
+                    event.stopPropagation();
+                }, className: classes.contrastColor },
+                React.createElement(MoreHorizIcon, null))),
+        menuEl ? (React.createElement(JBrowseMenu, { anchorEl: menuEl, menuItems: [
+                {
+                    label: 'Add to selection',
+                    onClick: () => {
+                        const r = treeToMap(tree).get(id);
+                        model.addToSelection(getAllChildren(r));
+                    },
+                },
+                {
+                    label: 'Remove from selection',
+                    onClick: () => {
+                        const r = treeToMap(tree).get(id);
+                        model.removeFromSelection(getAllChildren(r));
+                    },
+                },
+            ], onMenuItemClick: (_event, callback) => {
+                callback();
+                setMenuEl(null);
+            }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null));
+}
+//# sourceMappingURL=TrackCategory.js.map

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.js.map

@@ -0,0 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.d.ts

@@ -0,0 +1,11 @@
+/// <reference types="react" />
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { NodeData } from '../util';
+export interface InfoArgs {
+    target: HTMLElement;
+    id: string;
+    conf: AnyConfigurationModel;
+}
+export default function TrackLabel({ data }: {
+    data: NodeData;
+}): JSX.Element;

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js

@@ -0,0 +1,57 @@
+import React, { useState } from 'react';
+import { Checkbox, FormControlLabel, IconButton, Tooltip } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import JBrowseMenu from '@jbrowse/core/ui/Menu';
+import { getSession } from '@jbrowse/core/util';
+import { readConfObject, } from '@jbrowse/core/configuration';
+// icons
+import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
+// locals
+import { isUnsupported } from '../util';
+import { SanitizedHTML } from '@jbrowse/core/ui';
+const useStyles = makeStyles()(theme => ({
+    compactCheckbox: {
+        padding: 0,
+    },
+    checkboxLabel: {
+        marginRight: 0,
+        '&:hover': {
+            backgroundColor: theme.palette.action.selected,
+        },
+    },
+}));
+export default function TrackLabel({ data }) {
+    var _a, _b;
+    const { classes } = useStyles();
+    const { checked, conf, model, drawerPosition, id, name, onChange, selected } = data;
+    const [info, setInfo] = useState();
+    const description = (conf && readConfObject(conf, ['description'])) || '';
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
+            React.createElement(FormControlLabel, { className: classes.checkboxLabel, control: React.createElement(Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: isUnsupported(name), inputProps: {
+                        // @ts-ignore
+                        'data-testid': `htsTrackEntry-${id}`,
+                    } }), label: React.createElement("div", { style: { background: selected ? '#cccc' : undefined } },
+                    React.createElement(SanitizedHTML, { html: name })) })),
+        React.createElement(IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}` },
+            React.createElement(MoreHorizIcon, null)),
+        info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
+                ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) || []),
+                {
+                    label: 'Add to selection',
+                    onClick: () => model.addToSelection([info.conf]),
+                },
+                ...(selected
+                    ? [
+                        {
+                            label: 'Remove from selection',
+                            onClick: () => model.removeFromSelection([info.conf]),
+                        },
+                    ]
+                    : []),
+            ], onMenuItemClick: (_event, callback) => {
+                callback();
+                setInfo(undefined);
+            }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
+}
+//# sourceMappingURL=TrackLabel.js.map

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js.map

@@ -0,0 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="react" />
+import { NodeData } from '../util';
+export default function Node({ data, isOpen, style, setOpen, }: {
+    data: NodeData;
+    isOpen: boolean;
+    style?: {
+        height: number;
+    };
+    setOpen: (arg: boolean) => void;
+}): JSX.Element;

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.js

@@ -0,0 +1,48 @@
+import React from 'react';
+import { makeStyles } from 'tss-react/mui';
+// locals
+import Category from './TrackCategory';
+import TrackLabel from './TrackLabel';
+const useStyles = makeStyles()(theme => ({
+    // this accordionBase element's small padding is used to give a margin to
+    // accordionColor it a "margin" because the virtualized elements can't really
+    // use margin in a conventional way (it doesn't affect layout)
+    accordionBase: {
+        display: 'flex',
+    },
+    accordionCard: {
+        padding: 3,
+        cursor: 'pointer',
+        display: 'flex',
+    },
+    nestingLevelMarker: {
+        position: 'absolute',
+        borderLeft: '1.5px solid #555',
+    },
+    // accordionColor set's display:flex so that the child accordionText use
+    // vertically centered text
+    accordionColor: {
+        background: theme.palette.tertiary.main,
+        color: theme.palette.tertiary.contrastText,
+        width: '100%',
+        display: 'flex',
+        paddingLeft: 5,
+    },
+}));
+// An individual node in the track selector. Note: manually sets cursor:
+// pointer improves usability for what can be clicked
+export default function Node({ data, isOpen, style, setOpen, }) {
+    const { isLeaf, nestingLevel } = data;
+    const { classes } = useStyles();
+    const width = 10;
+    const marginLeft = nestingLevel * width + (isLeaf ? width : 0);
+    return (React.createElement("div", { style: style, className: !isLeaf ? classes.accordionBase : undefined },
+        new Array(nestingLevel).fill(0).map((_, idx) => (React.createElement("div", { key: `mark-${idx}`, style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }))),
+        React.createElement("div", { className: !isLeaf ? classes.accordionCard : undefined, style: {
+                marginLeft,
+                whiteSpace: 'nowrap',
+                width: '100%',
+            } },
+            React.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined }, !isLeaf ? (React.createElement(Category, { isOpen: isOpen, data: data, setOpen: setOpen })) : (React.createElement(TrackLabel, { data: data }))))));
+}
+//# sourceMappingURL=TrackListNode.js.map

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.js.map

@@ -0,0 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/util.d.ts

@@ -1,3 +1,19 @@
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { TreeNode } from '../model';
+import { HierarchicalTrackSelectorModel, TreeNode } from '../model';
+export interface NodeData {
+    nestingLevel: number;
+    checked: boolean;
+    conf: AnyConfigurationModel;
+    drawerPosition: unknown;
+    id: string;
+    isLeaf: boolean;
+    name: string;
+    onChange: Function;
+    toggleCollapse: (arg: string) => void;
+    tree: TreeNode;
+    selected: boolean;
+    model: HierarchicalTrackSelectorModel;
+}
 export declare function getAllChildren(subtree?: TreeNode): AnyConfigurationModel[];
+export declare function treeToMap(tree: TreeNode, map?: Map<string, TreeNode>): Map<string, TreeNode>;
+export declare function isUnsupported(name?: string): boolean;

package/esm/HierarchicalTrackSelectorWidget/components/util.js

@@ -2,4 +2,17 @@ export function getAllChildren(subtree) {
     // @ts-ignore
     return ((subtree === null || subtree === void 0 ? void 0 : subtree.children.map(t => t.children.length ? getAllChildren(t) : t.conf)) || []).flat(Infinity);
 }
+export function treeToMap(tree, map = new Map()) {
+    if (tree.id && tree.children.length) {
+        map.set(tree.id, tree);
+    }
+    for (let i = 0; i < tree.children.length; i++) {
+        const node = tree.children[i];
+        treeToMap(node, map);
+    }
+    return map;
+}
+export function isUnsupported(name = '') {
+    return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
+}
 //# sourceMappingURL=util.js.map

package/esm/HierarchicalTrackSelectorWidget/components/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACxB,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../../src/HierarchicalTrackSelectorWidget/components/util.ts"],"names":[],"mappings":"AAkBA,MAAM,UAAU,cAAc,CAAC,OAAkB;IAC/C,aAAa;IACb,OAAO,CACL,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CACxB,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC,CAAC,IAA8B,CAC1E,KAAI,EAAE,CACR,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;AAClB,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,IAAc,EAAE,MAAM,IAAI,GAAG,EAAoB;IACzE,IAAI,IAAI,CAAC,EAAE,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE;QACnC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;KACvB;IACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC7B,SAAS,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;KACrB;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,IAAI,GAAG,EAAE;IACrC,OAAO,IAAI,CAAC,QAAQ,CAAC,eAAe,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAA;AACrE,CAAC"}

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,6 +1,8 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { AbstractSessionModel } from '@jbrowse/core/util';
 import PluginManager from '@jbrowse/core/PluginManager';
+export declare function matches(query: string, conf: AnyConfigurationModel, session: AbstractSessionModel): any;
 export type TreeNode = {
     name: string;
     id: string;
@@ -16,7 +18,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
     collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
-    filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     selection: ({
@@ -24,7 +25,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    filterText: string;
 } & {
+    setSelection(elt: AnyConfigurationModel[]): void;
     addToSelection(elt: AnyConfigurationModel[]): void;
     removeFromSelection(elt: AnyConfigurationModel[]): void;
     clearSelection(): void;

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -6,11 +6,11 @@ import { ElementId } from '@jbrowse/core/util/types/mst';
 function hasAnyOverlap(a1 = [], a2 = []) {
     return !!a1.find(value => a2.includes(value));
 }
-function passesFilter(filter, config, session) {
-    const categories = readConfObject(config, 'category');
-    const filterLower = filter.toLowerCase();
-    return (getTrackName(config, session).toLowerCase().includes(filterLower) ||
-        !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(filterLower)).length));
+export function matches(query, conf, session) {
+    const categories = readConfObject(conf, 'category');
+    const queryLower = query.toLowerCase();
+    return (getTrackName(conf, session).toLowerCase().includes(queryLower) ||
+        !!(categories === null || categories === void 0 ? void 0 : categories.filter(c => c.toLowerCase().includes(queryLower)).length));
 }
 function filterTracks(tracks, self, assemblyName) {
     const { assemblyManager } = getSession(self);
@@ -34,7 +34,7 @@ export function generateHierarchy(model, trackConfigurations, collapsed, extra)
     const { filterText, view } = model;
     const session = getSession(model);
     trackConfigurations
-        .filter(conf => passesFilter(filterText, conf, session))
+        .filter(conf => matches(filterText, conf, session))
         .forEach(conf => {
         // copy the categories since this array can be mutated downstream
         const categories = [...(readConfObject(conf, 'category') || [])];
@@ -82,13 +82,16 @@ export default function stateTreeFactory(pluginManager) {
         id: ElementId,
         type: types.literal('HierarchicalTrackSelectorWidget'),
         collapsed: types.map(types.boolean),
-        filterText: '',
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
         selection: [],
+        filterText: '',
     }))
         .actions(self => ({
+        setSelection(elt) {
+            self.selection = elt;
+        },
         addToSelection(elt) {
             self.selection = dedupe([...self.selection, ...elt], e => e.trackId);
         },

package/esm/HierarchicalTrackSelectorWidget/model.js.map

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package/esm/PluginStoreWidget/components/InstalledPluginsList.js.map

@@ -1 +1 @@
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+{"version":3,"file":"InstalledPluginsList.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/InstalledPluginsList.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAGhD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAE/C,SAAS,oBAAoB,CAAC,EAC5B,aAAa,EACb,KAAK,GAIN;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,aAAa,CAAA;IAEjC,MAAM,WAAW,GAAG,OAAO;SACxB,MAAM,CAAC,CAAC,CAAC,EAAE,WAAC,OAAA,MAAA,aAAa,CAAC,cAAc,CAAC,CAAC,CAAC,IAAI,CAAC,0CAAE,MAAM,CAAA,EAAA,CAAC;SACzD,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAEnB,MAAM,eAAe,GAAG,OAAO,CAAC,MAAM,CACpC,MAAM,CAAC,EAAE,CAAC,CAAC,WAAW,CAAC,QAAQ,CAAC,MAAM,CAAC,IAAI,CAAC,CAC7C,CAAA;IAED,OAAO,CACL,oBAAC,IAAI,QACF,eAAe,CAAC,MAAM,CAAC,CAAC,CAAC,CACxB,eAAe;SACZ,MAAM,CAAC,MAAM,CAAC,EAAE,CACf,MAAM,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,CACnE;SACA,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CACb,oBAAC,eAAe,IACd,GAAG,EAAE,MAAM,CAAC,IAAI,EAChB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,KAAK,EACZ,aAAa,EAAE,aAAa,GAC5B,CACH,CAAC,CACL,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,yCAA4C,CACxD,CACI,CACR,CAAA;AACH,CAAC;AAED,eAAe,QAAQ,CAAC,oBAAoB,CAAC,CAAA"}

package/esm/PluginStoreWidget/components/PluginCard.d.ts

@@ -1,10 +1,9 @@
 /// <reference types="react" />
 import { JBrowsePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
-declare function PluginCard({ plugin, model, adminMode, }: {
+declare const _default: ({ plugin, model, adminMode, }: {
     plugin: JBrowsePlugin;
     model: PluginStoreModel;
     adminMode: boolean;
-}): JSX.Element;
-declare const _default: typeof PluginCard;
+}) => JSX.Element;
 export default _default;

package/esm/PluginStoreWidget/components/PluginCard.js

@@ -9,7 +9,7 @@ import { makeStyles } from 'tss-react/mui';
 import PersonIcon from '@mui/icons-material/Person';
 import AddIcon from '@mui/icons-material/Add';
 import CheckIcon from '@mui/icons-material/Check';
-const useStyles = makeStyles()(() => ({
+const useStyles = makeStyles()({
     card: {
         margin: '1em',
     },
@@ -25,8 +25,8 @@ const useStyles = makeStyles()(() => ({
         alignItems: 'center',
         margin: '0.4em 0em',
     },
-}));
-function PluginCard({ plugin, model, adminMode, }) {
+});
+export default observer(function PluginCard({ plugin, model, adminMode, }) {
     const { classes } = useStyles();
     const session = getSession(model);
     const { pluginManager } = getEnv(model);
@@ -47,7 +47,7 @@ function PluginCard({ plugin, model, adminMode, }) {
             React.createElement(Typography, { className: classes.bold }, "Description:"),
             React.createElement(Typography, null, plugin.description)),
         React.createElement(CardActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", disabled: disableButton, startIcon: isInstalled ? React.createElement(CheckIcon, null) : React.createElement(AddIcon, null), onClick: () => {
+            React.createElement(Button, { variant: "contained", disabled: disableButton, startIcon: isInstalled ? React.createElement(CheckIcon, null) : React.createElement(AddIcon, null), onClick: () => {
                     if (adminMode) {
                         jbrowse.addPlugin({ name: plugin.name, url: plugin.url });
                     }
@@ -56,6 +56,5 @@ function PluginCard({ plugin, model, adminMode, }) {
                     }
                     setTempDisabled(true);
                 } }, isInstalled ? 'Installed' : 'Install'))));
-}
-export default observer(PluginCard);
+});
 //# sourceMappingURL=PluginCard.js.map

package/esm/PluginStoreWidget/components/PluginCard.js.map

@@ -1 +1 @@
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+{"version":3,"file":"PluginCard.js","sourceRoot":"","sources":["../../../src/PluginStoreWidget/components/PluginCard.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AACvD,OAAO,EAEL,2BAA2B,GAC5B,MAAM,0BAA0B,CAAA;AACjC,OAAO,EACL,IAAI,EACJ,WAAW,EACX,WAAW,EACX,MAAM,EACN,IAAI,EACJ,UAAU,GACX,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,QAAQ;AACR,OAAO,UAAU,MAAM,4BAA4B,CAAA;AACnD,OAAO,OAAO,MAAM,yBAAyB,CAAA;AAC7C,OAAO,SAAS,MAAM,2BAA2B,CAAA;AAKjD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,IAAI,EAAE;QACJ,MAAM,EAAE,KAAK;KACd;IACD,IAAI,EAAE;QACJ,UAAU,EAAE,OAAO;QACnB,WAAW,EAAE,OAAO;KACrB;IACD,IAAI,EAAE;QACJ,UAAU,EAAE,GAAG;KAChB;IACD,SAAS,EAAE;QACT,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,MAAM,EAAE,WAAW;KACpB;CACF,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAC,SAAS,UAAU,CAAC,EAC1C,MAAM,EACN,KAAK,EACL,SAAS,GAKV;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IACvC,MAAM,WAAW,GAAG,OAAO,CACzB,aAAa,CAAC,wBAAwB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,KAAK,MAAM,CAAC,GAAG,CAAC,CAC3E,CAAA;IACD,MAAM,CAAC,YAAY,EAAE,eAAe,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACvD,MAAM,aAAa,GAAG,WAAW,IAAI,YAAY,CAAA;IAEjD,8DAA8D;IAC9D,MAAM,SAAS,GAAG,SAAS,CAAM,KAAK,EAAE,CAAC,CAAC,CAAA;IAC1C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,CAAA;IAE7B,OAAO,CACL,oBAAC,IAAI,IAAC,OAAO,EAAC,UAAU,EAAC,GAAG,EAAE,MAAM,CAAC,IAAI,EAAE,SAAS,EAAE,OAAO,CAAC,IAAI;QAChE,oBAAC,WAAW;YACV,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS;gBAC/B,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI;oBACtB,oBAAC,IAAI,IACH,IAAI,EAAE,GAAG,MAAM,CAAC,QAAQ,SAAS,EACjC,MAAM,EAAC,QAAQ,EACf,GAAG,EAAC,UAAU,IAEb,MAAM,CAAC,IAAI,CACP,CACI,CACT;YACN,6BAAK,SAAS,EAAE,OAAO,CAAC,SAAS;gBAC/B,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,GAAI;gBAC/C,oBAAC,UAAU,QAAE,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAc,CAChD;YACN,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,IAAI,mBAA2B;YAC9D,oBAAC,UAAU,QAAE,MAAM,CAAC,WAAW,CAAc,CACjC;QACd,oBAAC,WAAW;YACV,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,QAAQ,EAAE,aAAa,EACvB,SAAS,EAAE,WAAW,CAAC,CAAC,CAAC,oBAAC,SAAS,OAAG,CAAC,CAAC,CAAC,oBAAC,OAAO,OAAG,EACpD,OAAO,EAAE,GAAG,EAAE;oBACZ,IAAI,SAAS,EAAE;wBACb,OAAO,CAAC,SAAS,CAAC,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;qBAC1D;yBAAM,IAAI,2BAA2B,CAAC,OAAO,CAAC,EAAE;wBAC/C,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,CAAA;qBACjC;oBACD,eAAe,CAAC,IAAI,CAAC,CAAA;gBACvB,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAC/B,CACG,CACT,CACR,CAAA;AACH,CAAC,CAAC,CAAA"}

package/esm/PluginStoreWidget/components/PluginStoreWidget.js

@@ -18,7 +18,7 @@ const useStyles = makeStyles()(theme => ({
         margin: theme.spacing(1),
     },
     expandIcon: {
-        color: '#fff',
+        color: theme.palette.tertiary.contrastText,
     },
     adminBadge: {
         margin: '0.5em',
@@ -74,11 +74,11 @@ function PluginStoreWidget({ model }) {
                     React.createElement("code", null, "admin-server"),
                     ". Any changes you make will be saved to your configuration file. You also have the ability to add custom plugins that are not in the store."))),
             React.createElement("div", { className: classes.customPluginButton },
-                React.createElement(Button, { variant: "contained", color: "primary", onClick: () => setCustomPluginFormOpen(true) }, "Add custom plugin")),
+                React.createElement(Button, { variant: "contained", onClick: () => setCustomPluginFormOpen(true) }, "Add custom plugin")),
             React.createElement(CustomPluginForm, { open: customPluginFormOpen, onClose: () => setCustomPluginFormOpen(false), model: model }))),
         React.createElement(TextField, { label: "Filter plugins", value: model.filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
                 endAdornment: (React.createElement(InputAdornment, { position: "end" },
-                    React.createElement(IconButton, { color: "secondary", onClick: () => model.clearFilterText() },
+                    React.createElement(IconButton, { onClick: () => model.clearFilterText() },
                         React.createElement(ClearIcon, null)))),
             } }),
         React.createElement(Accordion, { defaultExpanded: true },

package/esm/PluginStoreWidget/components/PluginStoreWidget.js.map

@@ -1 +1 @@
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package/esm/ucsc-trackhub/ucscTrackHub.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ucscTrackHub.js","sourceRoot":"","sources":["../../src/ucsc-trackhub/ucscTrackHub.ts"],"names":[],"mappings":"AAEA,OAAO,EAAgB,aAAa,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC5E,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EACL,4BAA4B,EAC5B,wBAAwB,GACzB,MAAM,2BAA2B,CAAA;AAClC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAE7C,OAAO,EAAE,cAAc,EAAE,CAAA;AAEzB,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,WAAyB;IAC1D,IAAI;QACF,MAAM,WAAW,GAAG,MAAM,YAAY,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QACpE,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;QAClD,OAAO,IAAI,OAAO,CAAC,WAAW,CAAC,CAAA;KAChC;IAAC,OAAO,KAAK,EAAE;QACd,MAAM,IAAI,KAAK,CAAC,yCAAyC,KAAK,GAAG,CAAC,CAAA;KACnE;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,UAAwB;IAC7D,MAAM,eAAe,GAAG,MAAM,YAAY,CAAC,UAAU,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACvE,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;IACtD,OAAO,IAAI,WAAW,CAAC,eAAe,CAAC,CAAA;AACzC,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,UAAwB;IAC7D,MAAM,IAAI,GAAG,MAAM,YAAY,CAAC,UAAU,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5D,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAA;IACtD,OAAO,IAAI,WAAW,CAAC,IAAI,CAAC,CAAA;AAC9B,CAAC;AAED,MAAM,UAAU,OAAO,CAAC,KAAa,EAAE,IAAqB;IAC1D,OAAO;QACL,GAAG,EAAE,IAAI,GAAG,CAAC,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI;QAClC,YAAY,EAAE,aAAa;KAC5B,CAAA;AACH,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,KAAa,EAAE,GAAW,EAAE,IAAqB;IAC1E,OAAO,KAAK,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;AAC1D,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,KAAa,EAAE,GAAY;IAClD,OAAO,KAAK;QACV,CAAC,CAAC;YACE,GAAG,EAAE,KAAK;YACV,YAAY,EAAE,WAAW;SAC1B;QACH,CAAC,CAAC;YACE,GAAG,EAAE,GAAG;YACR,YAAY,EAAE,aAAa;SAC5B,CAAA;AACP,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,OAAoB,EACpB,UAAwB,EACxB,YAAoB,EACpB,eAAoB;IAEpB,MAAM,MAAM,GAAQ,EAAE,CAAA;IAEtB,OAAO,CAAC,OAAO,CAAC,CAAC,KAAK,EAAE,SAAS,EAAE,EAAE;;QACnC,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAA;QAC1C,MAAM,eAAe,GAAG;YACtB,YAAY;YACZ,gBAAgB;YAChB,WAAW;YACX,MAAM;SACP,CAAA;QACD,IAAI,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,eAAe,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE;YACxD,OAAM;SACP;QACD,MAAM,YAAY,GAAG,EAAE,CAAA;QACvB,IAAI,gBAAgB,GAAG,SAAS,CAAA;QAChC,GAAG;YACD,gBAAgB,GAAG,CAAA,MAAA,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,0CAAE,GAAG,CAAC,QAAQ,CAAC,KAAI,EAAE,CAAA;YACrE,IAAI,gBAAgB,EAAE;gBACpB,CAAC;gBAAA,CAAC,gBAAgB,CAAC,GAAG,gBAAgB,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBACjD,YAAY,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAA;aACjD;SACF,QAAQ,gBAAgB,EAAC;QAC1B,YAAY,CAAC,OAAO,EAAE,CAAA;QACtB,MAAM,UAAU,GAAG,YAAY;aAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,aAAD,CAAC,uBAAD,CAAC,CAAE,GAAG,CAAC,YAAY,CAAC,CAAC;aAC9B,MAAM,CAAC,CAAC,CAAC,EAAe,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAClC,MAAM,GAAG,GAAG,eAAe,CACzB,KAAK,EACL,UAAU,EACV,UAAU,EACV,OAAO,EACP,eAAe,CAChB,CAAA;QACD,MAAM,CAAC,IAAI,CAAC;YACV,GAAG,GAAG;YACN,OAAO,EAAE,iBAAiB,UAAU,CAAC,GAAG,CAAC,EAAE;YAC3C,aAAa,EAAE,CAAC,YAAY,CAAC;SAC9B,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;IAEF,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,eAAe,CACtB,KAAe,EACf,UAAoB,EACpB,UAAwB,EACxB,OAAoB,EACpB,eAAoB;;IAEpB,IAAI,SAAS,GAAG,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,CAAA;IAC1C,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC,IAAI,EAAE,CAAA;IAChD,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,cAAc,CAAC,IAAI,EAAE,CAAA;IAClD,MAAM,KAAK,GAAG,aAAa,CAAC,UAAU,CAAC,CAAA;IACvC,IAAI,CAAC,SAAS,EAAE;QACd,SAAS,GAAG,MAAA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,CAAC,0CAAE,GAAG,CAAC,MAAM,CAAC,CAAA;KAChE;IACD,IAAI,aAAa,GAAG,CAAA,SAAS,aAAT,SAAS,uBAAT,SAAS,CAAE,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,KAAI,EAAE,CAAA;IAClD,IAAI,aAAa,KAAK,KAAK,IAAI,UAAU,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE;QACxE,aAAa,GAAG,MAAM,CAAA;KACvB;IACD,MAAM,eAAe,GAAG,KAAK;QAC3B,CAAC,CAAC,OAAO,CAAC,UAAU,EAAE,UAAU,CAAC;QACjC,CAAC,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAA;IAExB,QAAQ,aAAa,EAAE;QACrB,KAAK,KAAK;YACR,OAAO;gBACL,IAAI,EAAE,iBAAiB;gBACvB,IAAI,EAAE,KAAK,CAAC,GAAG,CAAC,YAAY,CAAC;gBAC7B,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,YAAY;oBAClB,WAAW,EAAE,eAAe;oBAC5B,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK;4BACb,CAAC,CAAC,UAAU,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,EAAE,UAAU,CAAC;4BACzD,CAAC,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,MAAM,CAAC;qBAC9C;iBACF;aACF,CAAA;QAEH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;gBACD,QAAQ,EAAE;oBACR,IAAI,EAAE,oBAAoB;iBAC3B;aACF,CAAA;QACH,KAAK,QAAQ;YACX,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,aAAa;YAChB,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAAU;gBACpB,OAAO,EAAE;oBACP,IAAI,EAAE,eAAe;oBACrB,cAAc,EAAE,eAAe;iBAChC;aACF,CAAA;QACH,KAAK,UAAU;YACb,OAAO;gBACL,IAAI,EAAE,cAAc;gBACpB,IAAI;gBACJ,WAAW,EAAE,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC;gBACnC,QAAQ,EAAE,UAA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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.3.3",
+  "version": "2.4.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -39,6 +39,7 @@
   "dependencies": {
     "@gmod/ucsc-hub": "^0.1.6",
     "@mui/icons-material": "^5.0.1",
+    "@mui/x-data-grid": "^5.0.1",
     "clsx": "^1.1.0",
     "react-virtualized-auto-sizer": "^1.0.2",
     "react-vtree": "^3.0.0-beta.1",
@@ -60,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
+  "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
 }

package/src/AddConnectionWidget/components/ConnectionTypeSelect.tsx

@@ -33,7 +33,6 @@ function ConnectionTypeSelect(props: {
                     href={connectionType.url}
                     rel="noopener noreferrer"
                     target="_blank"
-                    color="secondary"
                   >
                     <OpenInNewIcon />
                   </IconButton>

package/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.tsx.snap

@@ -126,7 +126,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                   >
                     A track or assembly hub in the Track Hub format
                     <a
-                      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-colorSecondary MuiIconButton-sizeMedium css-1gws2xf-MuiButtonBase-root-MuiIconButton-root"
+                      class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
                       href="//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro"
                       rel="noopener noreferrer"
                       tabindex="0"

package/src/AddTrackWidget/components/DefaultAddTrackWorkflow.tsx

@@ -32,15 +32,12 @@ const useStyles = makeStyles()(theme => ({
     backgroundColor: theme.palette.background.default,
   },
   button: {
-    marginTop: theme.spacing(1),
     marginRight: theme.spacing(1),
   },
   actionsContainer: {
+    marginTop: theme.spacing(10),
     marginBottom: theme.spacing(2),
   },
-  stepContent: {
-    margin: theme.spacing(1),
-  },
   alertContainer: {
     padding: `${theme.spacing(2)}px 0px ${theme.spacing(2)}px 0px`,
   },

package/src/AddTrackWidget/components/TextIndexingConfig.tsx

@@ -68,7 +68,6 @@ const TextIndexingConfig = observer(({ model }: { model: AddTrackModel }) => {
                       endAdornment: (
                         <InputAdornment position="end">
                           <IconButton
-                            color="secondary"
                             onClick={() => {
                               const newAttr = section.values.filter((a, i) => {
                                 return i !== idx
@@ -113,7 +112,6 @@ const TextIndexingConfig = observer(({ model }: { model: AddTrackModel }) => {
                             }
                           }}
                           disabled={index === 0 ? value1 === '' : value2 === ''}
-                          color="secondary"
                           data-testid={`stringArrayAdd-Feat`}
                         >
                           <AddIcon />