@jbrowse/plugin-data-management 3.7.0 → 4.0.1

package/dist/UCSCTrackHubConnection/ucscTrackHub.d.ts

@@ -1,182 +0,0 @@
-import type { TrackDbFile } from '@gmod/ucsc-hub';
-import type { FileLocation } from '@jbrowse/core/util';
-export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }: {
-    trackDb: TrackDbFile;
-    trackDbLoc: FileLocation;
-    assemblyName: string;
-    sequenceAdapter: any;
-    baseUrl: string;
-}): ({
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string;
-    category: string[] | undefined;
-    metadata: {
-        html?: string | undefined;
-    };
-} | {
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string | undefined;
-    adapter: {
-        type: string;
-        bamLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        index: {
-            location: {
-                uri: string | undefined;
-                locationType: string;
-            };
-        };
-        cramLocation?: undefined;
-        craiLocation?: undefined;
-        sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
-        bigBedLocation?: undefined;
-        vcfGzLocation?: undefined;
-        hicLocation?: undefined;
-    };
-    metadata: {
-        html?: string | undefined;
-    };
-    category: (string | undefined)[];
-} | {
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string | undefined;
-    adapter: {
-        type: string;
-        cramLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        craiLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        sequenceAdapter: any;
-        bamLocation?: undefined;
-        index?: undefined;
-        bigWigLocation?: undefined;
-        bigBedLocation?: undefined;
-        vcfGzLocation?: undefined;
-        hicLocation?: undefined;
-    };
-    metadata: {
-        html?: string | undefined;
-    };
-    category: (string | undefined)[];
-} | {
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string | undefined;
-    adapter: {
-        type: string;
-        bigWigLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        bamLocation?: undefined;
-        index?: undefined;
-        cramLocation?: undefined;
-        craiLocation?: undefined;
-        sequenceAdapter?: undefined;
-        bigBedLocation?: undefined;
-        vcfGzLocation?: undefined;
-        hicLocation?: undefined;
-    };
-    metadata: {
-        html?: string | undefined;
-    };
-    category: (string | undefined)[];
-} | {
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string | undefined;
-    adapter: {
-        type: string;
-        bigBedLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        bamLocation?: undefined;
-        index?: undefined;
-        cramLocation?: undefined;
-        craiLocation?: undefined;
-        sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
-        vcfGzLocation?: undefined;
-        hicLocation?: undefined;
-    };
-    metadata: {
-        html?: string | undefined;
-    };
-    category: (string | undefined)[];
-} | {
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string | undefined;
-    adapter: {
-        type: string;
-        vcfGzLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        index: {
-            location: {
-                uri: string | undefined;
-                locationType: string;
-            };
-        };
-        bamLocation?: undefined;
-        cramLocation?: undefined;
-        craiLocation?: undefined;
-        sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
-        bigBedLocation?: undefined;
-        hicLocation?: undefined;
-    };
-    metadata: {
-        html?: string | undefined;
-    };
-    category: (string | undefined)[];
-} | {
-    trackId: string;
-    assemblyNames: string[];
-    type: string;
-    name: string;
-    description: string | undefined;
-    adapter: {
-        type: string;
-        hicLocation: {
-            uri: string | undefined;
-            locationType: string;
-        };
-        bamLocation?: undefined;
-        index?: undefined;
-        cramLocation?: undefined;
-        craiLocation?: undefined;
-        sequenceAdapter?: undefined;
-        bigWigLocation?: undefined;
-        bigBedLocation?: undefined;
-        vcfGzLocation?: undefined;
-    };
-    metadata: {
-        html?: string | undefined;
-    };
-    category: (string | undefined)[];
-})[];

package/dist/UCSCTrackHubConnection/ucscTrackHub.js

@@ -1,162 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.generateTracks = generateTracks;
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const util_2 = require("./util");
-function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }) {
-    const parentTrackKeys = new Set([
-        'superTrack',
-        'compositeTrack',
-        'container',
-        'view',
-    ]);
-    return Object.entries(trackDb.data)
-        .map(([trackName, track]) => {
-        var _a;
-        const { data } = track;
-        if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
-            return undefined;
-        }
-        else {
-            const parentTracks = [];
-            let currentTrackName = trackName;
-            do {
-                currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
-                if (currentTrackName) {
-                    currentTrackName = currentTrackName.split(' ')[0];
-                    parentTracks.push(trackDb.data[currentTrackName]);
-                }
-            } while (currentTrackName);
-            parentTracks.reverse();
-            return {
-                metadata: {
-                    ...track.data,
-                    ...(track.data.html
-                        ? {
-                            html: `<a href="${(0, util_2.resolve)(track.data.html, baseUrl)}">${track.data.html}</a>`,
-                        }
-                        : {}),
-                },
-                category: [
-                    track.data.group,
-                    ...parentTracks
-                        .map(p => p === null || p === void 0 ? void 0 : p.data.group)
-                        .filter((f) => !!f),
-                ].filter(f => !!f),
-                ...makeTrackConfig({
-                    track,
-                    trackDbLoc,
-                    trackDb,
-                    sequenceAdapter,
-                }),
-            };
-        }
-    })
-        .filter(util_1.notEmpty)
-        .map(r => ({
-        ...r,
-        trackId: `ucsc-trackhub-${(0, util_1.objectHash)(r)}`,
-        assemblyNames: [assemblyName],
-    }));
-}
-function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
-    var _a;
-    const { data } = track;
-    const parent = data.parent || '';
-    const bigDataUrl = data.bigDataUrl || '';
-    const bigDataIdx = data.bigDataIndex || '';
-    const trackType = data.type || ((_a = trackDb.data[parent]) === null || _a === void 0 ? void 0 : _a.data.type) || '';
-    const name = (data.shortLabel || '') + (bigDataUrl.includes('xeno') ? ' (xeno)' : '');
-    const isUri = (0, util_1.isUriLocation)(trackDbLoc);
-    let baseTrackType = trackType.split(' ')[0] || '';
-    if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
-        baseTrackType = 'cram';
-    }
-    const bigDataLocation = isUri
-        ? (0, util_2.makeLoc)(bigDataUrl, trackDbLoc)
-        : (0, util_2.makeLoc2)(bigDataUrl);
-    if (baseTrackType === 'bam') {
-        return {
-            type: 'AlignmentsTrack',
-            name,
-            description: data.longLabel,
-            adapter: {
-                type: 'BamAdapter',
-                bamLocation: bigDataLocation,
-                index: {
-                    location: isUri
-                        ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
-                        : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.bai`),
-                },
-            },
-        };
-    }
-    else if (baseTrackType === 'cram') {
-        return {
-            type: 'AlignmentsTrack',
-            name,
-            description: data.longLabel,
-            adapter: {
-                type: 'CramAdapter',
-                cramLocation: bigDataLocation,
-                craiLocation: isUri
-                    ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
-                    : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.crai`),
-                sequenceAdapter,
-            },
-        };
-    }
-    else if (baseTrackType === 'bigWig') {
-        return {
-            type: 'QuantitativeTrack',
-            name,
-            description: data.longLabel,
-            adapter: {
-                type: 'BigWigAdapter',
-                bigWigLocation: bigDataLocation,
-            },
-        };
-    }
-    else if (baseTrackType.startsWith('big')) {
-        return {
-            type: 'FeatureTrack',
-            name,
-            description: data.longLabel,
-            adapter: {
-                type: 'BigBedAdapter',
-                bigBedLocation: bigDataLocation,
-            },
-        };
-    }
-    else if (baseTrackType === 'vcfTabix') {
-        return {
-            type: 'VariantTrack',
-            name,
-            description: data.longLabel,
-            adapter: {
-                type: 'VcfTabixAdapter',
-                vcfGzLocation: bigDataLocation,
-                index: {
-                    location: isUri
-                        ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
-                        : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.tbi`),
-                },
-            },
-        };
-    }
-    else if (baseTrackType === 'hic') {
-        return {
-            type: 'HicTrack',
-            name,
-            description: data.longLabel,
-            adapter: {
-                type: 'HicAdapter',
-                hicLocation: bigDataLocation,
-            },
-        };
-    }
-    else {
-        return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType);
-    }
-}

package/dist/UCSCTrackHubConnection/util.d.ts

@@ -1,22 +0,0 @@
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
-import type { FileLocation } from '@jbrowse/core/util';
-export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
-export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
-export declare function makeLoc(first: string, base: {
-    uri: string;
-    baseUri?: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLocAlt(first: string, alt: string, base: {
-    uri: string;
-}): {
-    uri: string;
-    locationType: string;
-};
-export declare function makeLoc2(first: string, alt?: string): {
-    uri: string | undefined;
-    locationType: string;
-};
-export declare function resolve(uri: string, baseUri: string): string;

package/dist/UCSCTrackHubConnection/util.js

@@ -1,41 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchGenomesFile = fetchGenomesFile;
-exports.fetchTrackDbFile = fetchTrackDbFile;
-exports.makeLoc = makeLoc;
-exports.makeLocAlt = makeLocAlt;
-exports.makeLoc2 = makeLoc2;
-exports.resolve = resolve;
-const ucsc_hub_1 = require("@gmod/ucsc-hub");
-const io_1 = require("@jbrowse/core/util/io");
-async function fetchGenomesFile(genomesLoc) {
-    const genomesFileText = await (0, io_1.openLocation)(genomesLoc).readFile('utf8');
-    return new ucsc_hub_1.GenomesFile(genomesFileText);
-}
-async function fetchTrackDbFile(trackDbLoc) {
-    const text = await (0, io_1.openLocation)(trackDbLoc).readFile('utf8');
-    return new ucsc_hub_1.TrackDbFile(text);
-}
-function makeLoc(first, base) {
-    return {
-        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
-        locationType: 'UriLocation',
-    };
-}
-function makeLocAlt(first, alt, base) {
-    return first ? makeLoc(first, base) : makeLoc(alt, base);
-}
-function makeLoc2(first, alt) {
-    return first
-        ? {
-            uri: first,
-            locationType: 'LocalPath',
-        }
-        : {
-            uri: alt,
-            locationType: 'UriLocation',
-        };
-}
-function resolve(uri, baseUri) {
-    return new URL(uri, baseUri).href;
-}

package/dist/index.d.ts

@@ -1,20 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin';
-import type PluginManager from '@jbrowse/core/PluginManager';
-declare const AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
-    session: import("@jbrowse/core/util").AbstractSessionModel;
-    onClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element>;
-export default class DataManagementPlugin extends Plugin {
-    name: string;
-    exports: {
-        AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
-            session: import("@jbrowse/core/util").AbstractSessionModel;
-            onClose: () => void;
-        }) => import("react/jsx-runtime").JSX.Element>;
-    };
-    install(pluginManager: PluginManager): void;
-    configure(_pluginManager: PluginManager): void;
-}
-export { AssemblyManager };
-export type { AddTrackModel } from './AddTrackWidget/model';
-export type { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';

package/dist/index.js

@@ -1,68 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __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 });
-exports.AssemblyManager = void 0;
-const react_1 = require("react");
-const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const AddConnectionWidget_1 = __importDefault(require("./AddConnectionWidget"));
-const AddTrackWidget_1 = __importDefault(require("./AddTrackWidget"));
-const HierarchicalTrackSelectorWidget_1 = __importDefault(require("./HierarchicalTrackSelectorWidget"));
-const JB2TrackHubConnection_1 = __importDefault(require("./JB2TrackHubConnection"));
-const PluginStoreWidget_1 = __importDefault(require("./PluginStoreWidget"));
-const UCSCTrackHubConnection_1 = __importDefault(require("./UCSCTrackHubConnection"));
-const AssemblyManager = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AssemblyManager'))));
-exports.AssemblyManager = AssemblyManager;
-class DataManagementPlugin extends Plugin_1.default {
-    constructor() {
-        super(...arguments);
-        this.name = 'DataManagementPlugin';
-        this.exports = {
-            AssemblyManager,
-        };
-    }
-    install(pluginManager) {
-        (0, UCSCTrackHubConnection_1.default)(pluginManager);
-        (0, JB2TrackHubConnection_1.default)(pluginManager);
-        (0, AddTrackWidget_1.default)(pluginManager);
-        (0, HierarchicalTrackSelectorWidget_1.default)(pluginManager);
-        (0, AddConnectionWidget_1.default)(pluginManager);
-        (0, PluginStoreWidget_1.default)(pluginManager);
-    }
-    configure(_pluginManager) { }
-}
-exports.default = DataManagementPlugin;

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabelMenu.d.ts

@@ -1,11 +0,0 @@
-import type { HierarchicalTrackSelectorModel } from '../../model';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-declare const TrackLabelMenu: ({ id, trackId, stopPropagation, model, setOpen, conf, }: {
-    id: string;
-    trackId: string;
-    stopPropagation?: boolean;
-    conf: AnyConfigurationModel;
-    setOpen?: (arg: boolean) => void;
-    model: HierarchicalTrackSelectorModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default TrackLabelMenu;

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackListNode.d.ts

@@ -1,9 +0,0 @@
-import type { NodeData } from '../util';
-export default function Node({ data, isOpen, style, setOpen, }: {
-    data: NodeData;
-    isOpen: boolean;
-    style?: {
-        height: number;
-    };
-    setOpen: (arg: boolean) => void;
-}): import("react/jsx-runtime").JSX.Element;

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

@@ -1,36 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { makeStyles } from 'tss-react/mui';
-import Category from './TrackCategory';
-import TrackLabel from './TrackLabel';
-const useStyles = makeStyles()(theme => ({
-    accordionBase: {
-        display: 'flex',
-    },
-    accordionCard: {
-        padding: 3,
-        cursor: 'pointer',
-        display: 'flex',
-    },
-    nestingLevelMarker: {
-        position: 'absolute',
-        borderLeft: '1.5px solid #555',
-    },
-    accordionColor: {
-        background: theme.palette.tertiary.main,
-        color: theme.palette.tertiary.contrastText,
-        width: '100%',
-        display: 'flex',
-        paddingLeft: 5,
-    },
-}));
-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 (_jsxs("div", { style: style, className: !isLeaf ? classes.accordionBase : undefined, children: [new Array(nestingLevel).fill(0).map((_, idx) => (_jsx("div", { style: { left: idx * width + 4, height: style === null || style === void 0 ? void 0 : style.height }, className: classes.nestingLevelMarker }, `mark-${idx}`))), _jsx("div", { className: !isLeaf ? classes.accordionCard : undefined, style: {
-                    marginLeft,
-                    whiteSpace: 'nowrap',
-                    width: '100%',
-                }, children: _jsx("div", { className: !isLeaf ? classes.accordionColor : undefined, children: !isLeaf ? (_jsx(Category, { isOpen: isOpen, data: data, setOpen: setOpen })) : (_jsx(TrackLabel, { data: data })) }) })] }));
-}