@jbrowse/plugin-data-management 2.0.0 → 2.1.2

package/dist/ucsc-trackhub/ucscTrackHub.js

@@ -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

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package/esm/AddTrackWidget/components/AddTrackWidget.d.ts

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

package/esm/AddTrackWidget/components/AddTrackWidget.js

@@ -1,139 +1,26 @@
-import React, { useState } from 'react';
-import { Alert, Button, Step, StepContent, StepLabel, Stepper, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { getSession, isElectron, supportedIndexingAdapters, } from '@jbrowse/core/util';
-import { getConf } from '@jbrowse/core/configuration';
+import React from 'react';
 import { observer } from 'mobx-react';
+import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material';
+import { useLocalStorage } from '@jbrowse/core/util';
 import { getEnv } from 'mobx-state-tree';
-// locals
-import ConfirmTrack from './ConfirmTrack';
-import TrackSourceSelect from './TrackSourceSelect';
-const useStyles = makeStyles()(theme => ({
-    root: {
-        marginTop: theme.spacing(1),
-    },
-    stepper: {
-        backgroundColor: theme.palette.background.default,
-    },
-    button: {
-        marginTop: theme.spacing(1),
-        marginRight: theme.spacing(1),
-    },
-    actionsContainer: {
-        marginBottom: theme.spacing(2),
-    },
-    stepContent: {
-        margin: theme.spacing(1),
-    },
-    alertContainer: {
-        padding: `${theme.spacing(2)}px 0px ${theme.spacing(2)}px 0px`,
-    },
-}));
-const steps = ['Enter track data', 'Confirm track type'];
-function AddTrackWidget({ model }) {
-    const [activeStep, setActiveStep] = useState(0);
-    const { classes } = useStyles();
-    const session = getSession(model);
-    const { pluginManager } = getEnv(session);
-    const { rootModel } = pluginManager;
-    const { jobsManager } = rootModel;
-    const { assembly, trackAdapter, trackData, trackName, trackType, textIndexTrack, textIndexingConf, } = model;
-    const [trackErrorMessage, setTrackErrorMessage] = useState();
-    function getStepContent(step) {
-        switch (step) {
-            case 0:
-                return React.createElement(TrackSourceSelect, { model: model });
-            case 1:
-                return React.createElement(ConfirmTrack, { model: model });
-            default:
-                return React.createElement(Typography, null, "Unknown step");
-        }
-    }
-    async function handleNext() {
-        if (activeStep !== steps.length - 1) {
-            setActiveStep(activeStep + 1);
-            return;
-        }
-        const trackId = `${trackName
-            .toLowerCase()
-            .replace(/ /g, '_')}-${Date.now()}${session.adminMode ? '' : '-sessionTrack'}`;
-        const assemblyInstance = session.assemblyManager.get(assembly);
-        if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
-            // @ts-ignore
-            session.addTrackConf({
-                trackId,
-                type: trackType,
-                name: trackName,
-                assemblyNames: [assembly],
-                adapter: {
-                    ...trackAdapter,
-                    sequenceAdapter: getConf(assemblyInstance, ['sequence', 'adapter']),
-                },
-            });
-            const textSearchingDefault = {
-                attributes: ['Name', 'ID'],
-                exclude: ['CDS', 'exon'],
-            };
-            if (model.view) {
-                model.view.showTrack(trackId);
-                if (isElectron) {
-                    if (textIndexTrack && supportedIndexingAdapters(trackAdapter.type)) {
-                        const attr = textIndexingConf || textSearchingDefault;
-                        const indexName = trackName + '-index';
-                        const indexingParams = {
-                            ...attr,
-                            assemblies: [assembly],
-                            tracks: [trackId],
-                            indexType: 'perTrack',
-                            name: indexName,
-                            timestamp: new Date().toISOString(),
-                        };
-                        const newEntry = {
-                            indexingParams: indexingParams,
-                            name: indexName,
-                            cancelCallback: () => {
-                                jobsManager.abortJob();
-                            },
-                        };
-                        jobsManager.queueJob(newEntry);
-                    }
-                }
-            }
-            else {
-                session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
-            }
-            model.clearData();
-            // @ts-ignore
-            session.hideWidget(model);
-        }
-        else {
-            setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
-        }
-    }
-    function handleBack() {
-        setTrackErrorMessage(undefined);
-        setActiveStep(activeStep - 1);
-    }
-    function isNextDisabled() {
-        switch (activeStep) {
-            case 0:
-                return !trackData;
-            case 1:
-                return !(trackName && trackType && (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) && assembly);
-            default:
-                return true;
-        }
-    }
-    return (React.createElement("div", { className: classes.root },
-        React.createElement(Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical" }, steps.map((label, idx) => (React.createElement(Step, { key: label },
-            React.createElement(StepLabel, null, label),
-            React.createElement(StepContent, null,
-                getStepContent(idx),
-                React.createElement("div", { className: classes.actionsContainer },
-                    React.createElement(Button, { disabled: activeStep === 0, onClick: handleBack, className: classes.button }, "Back"),
-                    React.createElement(Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: handleNext, className: classes.button, "data-testid": "addTrackNextButton" }, activeStep === steps.length - 1 ? 'Add' : 'Next')),
-                trackErrorMessage ? (React.createElement("div", { className: classes.alertContainer },
-                    React.createElement(Alert, { severity: "error" }, trackErrorMessage))) : null)))))));
+import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow';
+function AddTrackSelector({ model }) {
+    const [val, setVal] = useLocalStorage('trackSelector-choice', 'Default');
+    const { pluginManager } = getEnv(model);
+    const widgets = pluginManager.getElementTypesInGroup('add track workflow');
+    const ComponentMap = {
+        Default: DefaultAddTrackWorkflow,
+        ...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 Component = ComponentMap[val2];
+    return (React.createElement(React.Fragment, null,
+        React.createElement(FormControl, null,
+            React.createElement(Select, { value: val2, onChange: event => setVal(event.target.value) }, Object.keys(ComponentMap).map(e => (React.createElement(MenuItem, { key: e, value: e }, e)))),
+            React.createElement(FormHelperText, null, "Type of add track workflow")),
+        React.createElement("br", null),
+        React.createElement(Component, { model: model })));
 }
-export default observer(AddTrackWidget);
+export default observer(AddTrackSelector);
 //# sourceMappingURL=AddTrackWidget.js.map

package/esm/AddTrackWidget/components/AddTrackWidget.js.map

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package/esm/AddTrackWidget/components/ConfirmTrack.js

@@ -141,13 +141,10 @@ const TextIndexingConfig = observer(({ model }) => {
 });
 const TrackAdapterSelector = observer(({ model }) => {
     const { classes } = useStyles();
-    const session = getSession(model);
     const { trackAdapter } = model;
-    // prettier-ignore
-    const adapters = getAdapterTypes(getEnv(session).pluginManager);
-    return (React.createElement(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: {
+    const { pluginManager } = getEnv(model);
+    const adapters = getAdapterTypes(pluginManager);
+    return (React.createElement(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' },
         } },
@@ -164,6 +161,8 @@ const TrackAdapterSelector = observer(({ model }) => {
                 ? (_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 }) {

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

@@ -1 +1 @@
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package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWorkflow({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWorkflow;
+export default _default;