npm - @jbrowse/plugin-data-management - Versions diffs - 2.1.0 → 2.1.3 - Mend

@jbrowse/plugin-data-management 2.1.0 → 2.1.3

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Files changed (93) hide show

package/dist/ucsc-trackhub/ucscTrackHub.js CHANGED Viewed

@@ -22,155 +22,66 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __setModuleDefault(result, mod);
     return result;
 };
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __read = (this && this.__read) || function (o, n) {
-    var m = typeof Symbol === "function" && o[Symbol.iterator];
-    if (!m) return o;
-    var i = m.call(o), r, ar = [], e;
-    try {
-        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
-    }
-    catch (error) { e = { error: error }; }
-    finally {
-        try {
-            if (r && !r.done && (m = i["return"])) m.call(i);
-        }
-        finally { if (e) throw e.error; }
-    }
-    return ar;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.generateTracks = exports.fetchTrackDbFile = exports.fetchGenomesFile = exports.fetchHubFile = exports.ucscAssemblies = void 0;
-var util_1 = require("@jbrowse/core/util");
-var io_1 = require("@jbrowse/core/util/io");
-var tracks_1 = require("@jbrowse/core/util/tracks");
-var ucscAssemblies_1 = __importDefault(require("./ucscAssemblies"));
+const util_1 = require("@jbrowse/core/util");
+const io_1 = require("@jbrowse/core/util/io");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const ucscAssemblies_1 = __importDefault(require("./ucscAssemblies"));
 exports.ucscAssemblies = ucscAssemblies_1.default;
-function fetchHubFile(hubFileLocation) {
-    return __awaiter(this, void 0, void 0, function () {
-        var hubFileText, HubFile, error_1;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    _a.trys.push([0, 3, , 4]);
-                    return [4 /*yield*/, (0, io_1.openLocation)(hubFileLocation).readFile('utf8')];
-                case 1:
-                    hubFileText = _a.sent();
-                    return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('@gmod/ucsc-hub')); })];
-                case 2:
-                    HubFile = (_a.sent()).HubFile;
-                    return [2 /*return*/, new HubFile(hubFileText)];
-                case 3:
-                    error_1 = _a.sent();
-                    throw new Error("Not a valid hub.txt file, got error: '".concat(error_1, "'"));
-                case 4: return [2 /*return*/];
-            }
-        });
-    });
+async function fetchHubFile(hubFileLocation) {
+    try {
+        const hubFileText = await (0, io_1.openLocation)(hubFileLocation).readFile('utf8');
+        const { HubFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
+        return new HubFile(hubFileText);
+    }
+    catch (error) {
+        throw new Error(`Not a valid hub.txt file, got error: '${error}'`);
+    }
 }
 exports.fetchHubFile = fetchHubFile;
-function fetchGenomesFile(genomesFileLocation) {
-    return __awaiter(this, void 0, void 0, function () {
-        var genomesFileText, GenomesFile;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, (0, io_1.openLocation)(genomesFileLocation).readFile('utf8')];
-                case 1:
-                    genomesFileText = _a.sent();
-                    return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('@gmod/ucsc-hub')); })];
-                case 2:
-                    GenomesFile = (_a.sent()).GenomesFile;
-                    return [2 /*return*/, new GenomesFile(genomesFileText)];
-            }
-        });
-    });
+async function fetchGenomesFile(genomesFileLocation) {
+    const genomesFileText = await (0, io_1.openLocation)(genomesFileLocation).readFile('utf8');
+    const { GenomesFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
+    return new GenomesFile(genomesFileText);
 }
 exports.fetchGenomesFile = fetchGenomesFile;
-function fetchTrackDbFile(trackDbFileLocation) {
-    return __awaiter(this, void 0, void 0, function () {
-        var text, TrackDbFile;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0: return [4 /*yield*/, (0, io_1.openLocation)(trackDbFileLocation).readFile('utf8')];
-                case 1:
-                    text = _a.sent();
-                    return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('@gmod/ucsc-hub')); })];
-                case 2:
-                    TrackDbFile = (_a.sent()).TrackDbFile;
-                    return [2 /*return*/, new TrackDbFile(text)];
-            }
-        });
-    });
+async function fetchTrackDbFile(trackDbFileLocation) {
+    const text = await (0, io_1.openLocation)(trackDbFileLocation).readFile('utf8');
+    const { TrackDbFile } = await Promise.resolve().then(() => __importStar(require('@gmod/ucsc-hub')));
+    return new TrackDbFile(text);
 }
 exports.fetchTrackDbFile = fetchTrackDbFile;
 function generateTracks(trackDb, trackDbFileLocation, assemblyName, sequenceAdapter) {
-    var tracks = [];
-    trackDb.forEach(function (track, trackName) {
-        var _a;
-        var trackKeys = Array.from(track.keys());
-        var parentTrackKeys = [
+    const tracks = [];
+    trackDb.forEach((track, trackName) => {
+        const trackKeys = Array.from(track.keys());
+        const parentTrackKeys = [
             'superTrack',
             'compositeTrack',
             'container',
             'view',
         ];
-        if (trackKeys.some(function (key) { return parentTrackKeys.includes(key); })) {
+        if (trackKeys.some(key => parentTrackKeys.includes(key))) {
             return;
         }
-        var parentTracks = [];
-        var currentTrackName = trackName;
+        const parentTracks = [];
+        let currentTrackName = trackName;
         do {
             currentTrackName = trackDb.get(currentTrackName).get('parent');
             if (currentTrackName) {
                 ;
-                _a = __read(currentTrackName.split(' '), 1), currentTrackName = _a[0];
+                [currentTrackName] = currentTrackName.split(' ');
                 parentTracks.push(trackDb.get(currentTrackName));
             }
         } while (currentTrackName);
         parentTracks.reverse();
-        var categories = parentTracks.map(function (parentTrack) {
-            return parentTrack.get('shortLabel');
-        });
-        var res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
-        res.trackId = "ucsc-trackhub-".concat((0, util_1.objectHash)(res));
+        const categories = parentTracks.map(parentTrack => parentTrack.get('shortLabel'));
+        const res = makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter);
+        res.trackId = `ucsc-trackhub-${(0, util_1.objectHash)(res)}`;
         res.assemblyNames = [assemblyName];
         tracks.push(res);
     });
@@ -178,16 +89,16 @@ function generateTracks(trackDb, trackDbFileLocation, assemblyName, sequenceAdap
 }
 exports.generateTracks = generateTracks;
 function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequenceAdapter) {
-    var trackType = track.get('type');
+    let trackType = track.get('type');
     if (!trackType) {
         trackType = trackDb.get(track.get('parent')).get('type');
     }
-    var baseTrackType = trackType.split(' ')[0];
+    let baseTrackType = trackType.split(' ')[0];
     if (baseTrackType === 'bam' &&
         track.get('bigDataUrl').toLowerCase().endsWith('cram')) {
         baseTrackType = 'cram';
     }
-    var bigDataLocation;
+    let bigDataLocation;
     if (trackDbFileLocation.uri) {
         bigDataLocation = {
             uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
@@ -200,7 +111,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
             locationType: 'LocalPathLocation',
         };
     }
-    var bigDataIndexLocation;
+    let bigDataIndexLocation;
     switch (baseTrackType) {
         case 'bam':
             if (trackDbFileLocation.uri) {
@@ -211,7 +122,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                         locationType: 'UriLocation',
                     }
                     : {
-                        uri: new URL("".concat(track.get('bigDataUrl'), ".bai"), trackDbFileLocation.uri).href,
+                        uri: new URL(`${track.get('bigDataUrl')}.bai`, trackDbFileLocation.uri).href,
                         locationType: 'UriLocation',
                     };
             }
@@ -222,7 +133,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                         locationType: 'LocalPathLocation',
                     }
                     : {
-                        localPath: "".concat(track.get('bigDataUrl'), ".bai"),
+                        localPath: `${track.get('bigDataUrl')}.bai`,
                         locationType: 'LocalPathLocation',
                     };
             }
@@ -363,7 +274,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                         locationType: 'UriLocation',
                     }
                     : {
-                        uri: new URL("".concat(track.get('bigDataUrl'), ".crai"), trackDbFileLocation.uri).href,
+                        uri: new URL(`${track.get('bigDataUrl')}.crai`, trackDbFileLocation.uri).href,
                         locationType: 'UriLocation',
                     };
             }
@@ -374,7 +285,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                         locationType: 'LocalPathLocation',
                     }
                     : {
-                        localPath: "".concat(track.get('bigDataUrl'), ".crai"),
+                        localPath: `${track.get('bigDataUrl')}.crai`,
                         locationType: 'LocalPathLocation',
                     };
             }
@@ -387,7 +298,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                     type: 'CramAdapter',
                     cramLocation: bigDataLocation,
                     craiLocation: bigDataIndexLocation,
-                    sequenceAdapter: sequenceAdapter,
+                    sequenceAdapter,
                 },
             };
         case 'gvf':
@@ -418,7 +329,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                         locationType: 'UriLocation',
                     }
                     : {
-                        uri: new URL("".concat(track.get('bigDataUrl'), ".tbi"), trackDbFileLocation.uri).href,
+                        uri: new URL(`${track.get('bigDataUrl')}.tbi`, trackDbFileLocation.uri).href,
                         locationType: 'UriLocation',
                     };
             }
@@ -429,7 +340,7 @@ function makeTrackConfig(track, categories, trackDbFileLocation, trackDb, sequen
                         locationType: 'LocalPathLocation',
                     }
                     : {
-                        localPath: "".concat(track.get('bigDataUrl'), ".tbi"),
+                        localPath: `${track.get('bigDataUrl')}.tbi`,
                         locationType: 'LocalPathLocation',
                     };
             }

package/dist/ucsc-trackhub/ucscTrackHub.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/HierarchicalTrackSelectorWidget/components/Node.js CHANGED Viewed

@@ -9,53 +9,48 @@ import JBrowseMenu from '@jbrowse/core/ui/Menu';
 import { getSession } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { getAllChildren } from './util';
-const useStyles = makeStyles()(theme => {
-    var _a, _b;
-    return ({
-        compactCheckbox: {
-            padding: 0,
-        },
-        checkboxLabel: {
-            marginRight: 0,
-            '&:hover': {
-                backgroundColor: '#eee',
-            },
-        },
-        contrastColor: {
-            color: theme.palette.secondary.contrastText,
-        },
-        // 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: {
-            // @ts-ignore
-            background: (_a = theme.palette.tertiary) === null || _a === void 0 ? void 0 : _a.main,
-            // @ts-ignore
-            color: (_b = theme.palette.tertiary) === null || _b === void 0 ? void 0 : _b.contrastText,
-            width: '100%',
-            display: 'flex',
-            paddingLeft: 5,
-        },
-        // margin:auto 0 to center text vertically
-        accordionText: {
-            margin: 'auto 0',
+const useStyles = makeStyles()(theme => ({
+    compactCheckbox: {
+        padding: 0,
+    },
+    checkboxLabel: {
+        marginRight: 0,
+        '&:hover': {
+            backgroundColor: '#eee',
         },
-    });
-});
+    },
+    contrastColor: {
+        color: theme.palette.secondary.contrastText,
+    },
+    // 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,
+    },
+    // margin:auto 0 to center text vertically
+    accordionText: {
+        margin: 'auto 0',
+    },
+}));
 function treeToMap(tree, map = new Map()) {
     if (tree.id && tree.children.length) {
         map.set(tree.id, tree);

package/esm/HierarchicalTrackSelectorWidget/components/Node.js.map CHANGED Viewed

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package/esm/HierarchicalTrackSelectorWidget/model.js CHANGED Viewed

@@ -16,7 +16,8 @@ function getTrackName(config) {
         throw new Error('not a track');
     }
     return (readConfObject(config, 'name') ||
-        `Reference sequence (${readConfObject(getParent(config), 'name')})`);
+        `Reference sequence (${readConfObject(getParent(config), 'displayName') ||
+            readConfObject(getParent(config), 'name')})`);
 }
 function filterTracks(tracks, self, assemblyName) {
     const { assemblyManager } = getSession(self);

package/esm/HierarchicalTrackSelectorWidget/model.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/HierarchicalTrackSelectorWidget/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,SAAS,EAAE,MAAM,EAAY,MAAM,iBAAiB,CAAA;AACpE,OAAO,EACL,OAAO,EACP,cAAc,GAEf,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAC/C,OAAO,EAAE,SAAS,EAAE,MAAM,8BAA8B,CAAA;AAGxD,SAAS,aAAa,CAAI,KAAU,EAAE,EAAE,KAAU,EAAE;IAClD,OAAO,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAA;AAC/C,CAAC;AAED,SAAS,YAAY,CAAC,MAAc,EAAE,MAA6B;IACjE,MAAM,UAAU,GAAG,cAAc,CAAC,MAAM,EAAE,UAAU,CAAyB,CAAA;IAC7E,MAAM,WAAW,GAAG,MAAM,CAAC,WAAW,EAAE,CAAA;IACxC,OAAO,CACL,YAAY,CAAC,MAAM,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;QACxD,CAAC,CAAC,CAAA,UAAU,aAAV,UAAU,uBAAV,UAAU,CAAE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,MAAM,CAAA,CACxE,CAAA;AACH,CAAC;AAED,SAAS,YAAY,CAAC,MAA6B;IACjD,IAAI,CAAC,MAAM,CAAC,OAAO,EAAE;QACnB,MAAM,IAAI,KAAK,CAAC,aAAa,CAAC,CAAA;KAC/B;IACD,OAAO,CACL,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC;QAC9B,uBACE,cAAc,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,aAAa,CAAC;YAChD,cAAc,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,MAAM,CAC1C,GAAG,CACJ,CAAA;AACH,CAAC;AAWD,SAAS,YAAY,CACnB,MAA+B,EAC/B,IAAgC,EAChC,YAAoB;IAEpB,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,CAAC,IAAI,CAAC,CAAA;IACtC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAElD,IAAI,CAAC,QAAQ,EAAE;QACb,OAAO,EAAE,CAAA;KACV;IACD,OAAO,MAAM;SACV,MAAM,CAAC,CAAC,CAAC,EAAE;QACV,MAAM,mBAAmB,GAAG,cAAc,CAAC,CAAC,EAAE,eAAe,CAAC,CAAA;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,QAAQ,CAAA;QAC/B,OAAO,aAAa,CAAC,UAAU,EAAE,mBAAmB,CAAC,CAAA;IACvD,CAAC,CAAC;SACD,MAAM,CAAC,CAAC,CAAC,EAAE;QACV,MAAM,EAAE,YAAY,EAAE,GAAG,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAClE,MAAM,cAAc,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,CAAmB,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACxE,MAAM,aAAa,GAAG,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAmB,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;QACrE,OAAO,aAAa,CAAC,cAAc,EAAE,aAAa,CAAC,CAAA;IACrD,CAAC,CAAC,CAAA;AACN,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,KAAqC,EACrC,mBAA4C,EAC5C,SAAwD;IAExD,MAAM,SAAS,GAAG,EAAE,QAAQ,EAAE,EAAgB,EAAc,CAAA;IAC5D,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IAElC,mBAAmB;SAChB,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,YAAY,CAAC,UAAU,EAAE,IAAI,CAAC,CAAC;SAC9C,OAAO,CAAC,IAAI,CAAC,EAAE;QACd,iEAAiE;QACjE,MAAM,UAAU,GAAG,CAAC,GAAG,CAAC,cAAc,CAAC,IAAI,EAAE,UAAU,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;QAEhE,uEAAuE;QACvE,kEAAkE;QAClE,0BAA0B;QAC1B,IAAI,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE;YACzC,UAAU,CAAC,OAAO,CAAC,iBAAiB,CAAC,CAAA;SACtC;QAED,IAAI,SAAS,GAAG,SAAS,CAAA;QAEzB,wDAAwD;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;YAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YAC9B,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAA;YAC7D,MAAM,EAAE,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;YAC/C,IAAI,CAAC,GAAG,EAAE;gBACR,MAAM,CAAC,GAAG;oBACR,QAAQ,EAAE,EAAE;oBACZ,IAAI,EAAE,QAAQ;oBACd,EAAE;oBACF,eAAe,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC;iBACpC,CAAA;gBACD,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;gBAC1B,SAAS,GAAG,CAAC,CAAA;aACd;iBAAM;gBACL,SAAS,GAAG,GAAG,CAAA;aAChB;SACF;QACD,MAAM,MAAM,GAAG,IAAI,CAAC,MAAoD,CAAA;QAExE,uEAAuE;QACvE,SAAS,CAAC,QAAQ,CAAC,MAAM,CACvB,SAAS,CAAC,QAAQ,CAAC,SAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,QAAQ,CAAC,MAAM,CAAC,EACxD,CAAC,EACD;YACE,EAAE,EAAE,IAAI,CAAC,OAAO;YAChB,IAAI,EAAE,YAAY,CAAC,IAAI,CAAC;YACxB,IAAI;YACJ,OAAO,EAAE,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,IAAI,CAAC;YACrD,QAAQ,EAAE,EAAE;SACb,CACF,CAAA;IACH,CAAC,CAAC,CAAA;IAEJ,OAAO,SAAS,CAAC,QAAQ,CAAA;AAC3B,CAAC;AAED,MAAM,CAAC,OAAO,UAAU,gBAAgB,CAAC,aAA4B;IACnE,OAAO,KAAK;SACT,KAAK,CAAC,iCAAiC,EAAE;QACxC,EAAE,EAAE,SAAS;QACb,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,iCAAiC,CAAC;QACtD,SAAS,EAAE,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC;QACnC,UAAU,EAAE,EAAE;QACd,IAAI,EAAE,KAAK,CAAC,aAAa,CACvB,aAAa,CAAC,gBAAgB,CAAC,MAAM,EAAE,YAAY,CAAC,CACrD;KACF,CAAC;SACD,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,SAAS,EAAE,EAA6B;KACzC,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB,cAAc,CAAC,GAA4B;YACzC,IAAI,CAAC,SAAS,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,EAAE,GAAG,GAAG,CAAC,CAAA;QAC9C,CAAC;QACD,mBAAmB,CAAC,GAA4B;YAC9C,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAA;QAC/D,CAAC;QACD,cAAc;YACZ,IAAI,CAAC,SAAS,GAAG,EAAE,CAAA;QACrB,CAAC;QACD,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD,cAAc,CAAC,QAAgB;YAC7B,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC7D,CAAC;QACD,eAAe;YACb,IAAI,CAAC,UAAU,GAAG,EAAE,CAAA;QACtB,CAAC;QACD,aAAa,CAAC,OAAe;YAC3B,IAAI,CAAC,UAAU,GAAG,OAAO,CAAA;QAC3B,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd,kBAAkB,CAAC,YAAoB;YACrC,MAAM,EAAE,eAAe,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YAC5C,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,MAAM,SAAS,GAAG,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,aAAa,CAAC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package/esm/PluginStoreWidget/components/PluginStoreWidget.js CHANGED Viewed

@@ -22,8 +22,7 @@ const useStyles = makeStyles()(theme => ({
     adminBadge: {
         margin: '0.5em',
         borderRadius: 3,
-        // this is the quaternary color in JB2 palette
-        backgroundColor: '#FFB11D',
+        backgroundColor: theme.palette.quaternary.main,
         padding: '1em',
         display: 'flex',
         alignContent: 'center',

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

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.1.0",
+  "version": "2.1.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -37,7 +37,6 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@gmod/ucsc-hub": "^0.1.3",
     "@mui/icons-material": "^5.0.1",
     "clsx": "^1.1.0",
@@ -62,5 +61,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "0db0462fa1f9f15ab4869da085bcab032b9483c3"
+  "gitHead": "ebd548ceb52adb36cf6ab437082b5b5feac1338e"
 }

package/src/AddConnectionWidget/components/__snapshots__/AddConnectionWidget.test.js.snap CHANGED Viewed

@@ -14,7 +14,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
         class="MuiStepLabel-root MuiStepLabel-vertical css-14sza3e-MuiStepLabel-root"
       >
         <span
-          class="MuiStepLabel-iconContainer css-vnkopk-MuiStepLabel-iconContainer"
+          class="MuiStepLabel-iconContainer Mui-active css-vnkopk-MuiStepLabel-iconContainer"
         >
           <svg
             aria-hidden="true"
@@ -68,7 +68,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                   class="MuiFormControl-root MuiFormControl-fullWidth MuiTextField-root css-wb57ya-MuiFormControl-root-MuiTextField-root"
                 >
                   <label
-                    class="MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined MuiFormLabel-root MuiFormLabel-colorPrimary MuiFormLabel-filled css-1sumxir-MuiFormLabel-root-MuiInputLabel-root"
+                    class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-shrink MuiInputLabel-outlined MuiFormLabel-colorPrimary MuiFormLabel-filled css-1sumxir-MuiFormLabel-root-MuiInputLabel-root"
                     data-shrink="true"
                     for="mui-1"
                     id="mui-1-label"
@@ -76,15 +76,14 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                     connectionType
                   </label>
                   <div
-                    class="MuiOutlinedInput-root MuiInputBase-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl css-md26zr-MuiInputBase-root-MuiOutlinedInput-root"
-                    variant="outlined"
+                    class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-colorPrimary MuiInputBase-fullWidth MuiInputBase-formControl css-md26zr-MuiInputBase-root-MuiOutlinedInput-root"
                   >
                     <div
                       aria-describedby="mui-1-helper-text"
                       aria-expanded="false"
                       aria-haspopup="listbox"
                       aria-labelledby="mui-1-label mui-1"
-                      class="MuiSelect-select MuiSelect-outlined MuiOutlinedInput-input MuiInputBase-input css-11u53oe-MuiSelect-select-MuiInputBase-input-MuiOutlinedInput-input"
+                      class="MuiSelect-select MuiSelect-outlined MuiInputBase-input MuiOutlinedInput-input css-11u53oe-MuiSelect-select-MuiInputBase-input-MuiOutlinedInput-input"
                       id="mui-1"
                       role="button"
                       tabindex="0"
@@ -155,7 +154,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                 class="tss-1spe31o-actionsContainer"
               >
                 <button
-                  class="MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeMedium MuiButton-textSizeMedium MuiButtonBase-root Mui-disabled tss-11xjtta-button css-1e6y48t-MuiButtonBase-root-MuiButton-root"
+                  class="MuiButtonBase-root Mui-disabled MuiButton-root MuiButton-text MuiButton-textPrimary MuiButton-sizeMedium MuiButton-textSizeMedium tss-11xjtta-button css-1e6y48t-MuiButtonBase-root-MuiButton-root"
                   disabled=""
                   tabindex="-1"
                   type="button"
@@ -163,7 +162,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
                   Back
                 </button>
                 <button
-                  class="MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButtonBase-root tss-11xjtta-button css-sghohy-MuiButtonBase-root-MuiButton-root"
+                  class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium tss-11xjtta-button css-sghohy-MuiButtonBase-root-MuiButton-root"
                   data-testid="addConnectionNext"
                   tabindex="0"
                   type="button"
@@ -193,7 +192,7 @@ exports[`<AddConnectionWidget /> renders 1`] = `
         class="MuiStepLabel-root MuiStepLabel-vertical Mui-disabled css-14sza3e-MuiStepLabel-root"
       >
         <span
-          class="MuiStepLabel-iconContainer css-vnkopk-MuiStepLabel-iconContainer"
+          class="MuiStepLabel-iconContainer Mui-disabled css-vnkopk-MuiStepLabel-iconContainer"
         >
           <svg
             aria-hidden="true"