@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/dist/ucsc-trackhub/ucscTrackHub.js

@@ -1,208 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ucscAssemblies = void 0;
-exports.fetchGenomesFile = fetchGenomesFile;
-exports.fetchTrackDbFile = fetchTrackDbFile;
-exports.makeLoc = makeLoc;
-exports.makeLocAlt = makeLocAlt;
-exports.makeLoc2 = makeLoc2;
-exports.generateTracks = generateTracks;
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const ucsc_hub_1 = require("@gmod/ucsc-hub");
-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 generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }) {
-    return Object.entries(trackDb.data)
-        .map(([trackName, track]) => {
-        var _a;
-        const trackKeys = Object.keys(track);
-        const parentTrackKeys = new Set([
-            'superTrack',
-            'compositeTrack',
-            'container',
-            'view',
-        ]);
-        if (trackKeys.some(key => parentTrackKeys.has(key))) {
-            return undefined;
-        }
-        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();
-        const categories = parentTracks
-            .map(p => p === null || p === void 0 ? void 0 : p.data.shortLabel)
-            .filter((f) => !!f);
-        const res = makeTrackConfig({
-            track: track,
-            categories,
-            trackDbLoc,
-            trackDb,
-            sequenceAdapter,
-        });
-        return {
-            ...res,
-            trackId: `ucsc-trackhub-${(0, util_1.objectHash)(res)}`,
-            assemblyNames: [assemblyName],
-        };
-    })
-        .filter(util_1.notEmpty);
-}
-function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapter, }) {
-    var _a;
-    const trackType = track.data.type || ((_a = trackDb.data[track.data.parent || '']) === null || _a === void 0 ? void 0 : _a.data.type) || '';
-    const name = track.data.shortLabel || '';
-    const bigDataUrl = track.data.bigDataUrl || '';
-    const bigDataIdx = track.data.bigDataIndex || '';
-    const isUri = (0, util_1.isUriLocation)(trackDbLoc);
-    let baseTrackType = trackType.split(' ')[0] || '';
-    if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
-        baseTrackType = 'cram';
-    }
-    const bigDataLocation = isUri
-        ? makeLoc(bigDataUrl, trackDbLoc)
-        : makeLoc2(bigDataUrl);
-    switch (baseTrackType) {
-        case 'bam':
-            return {
-                type: 'AlignmentsTrack',
-                name: track.data.longLabel,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BamAdapter',
-                    bamLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
-                    },
-                },
-            };
-        case 'cram':
-            return {
-                type: 'AlignmentsTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'CramAdapter',
-                    cramLocation: bigDataLocation,
-                    craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
-                        : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
-                    sequenceAdapter,
-                },
-            };
-        case 'bigBarChart':
-        case 'bigBed':
-        case 'bigGenePred':
-        case 'bigChain':
-        case 'bigInteract':
-        case 'bigMaf':
-        case 'bigNarrowPeak':
-        case 'bigPsl':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
-        case 'bigWig':
-            return {
-                type: 'QuantitativeTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigWigAdapter',
-                    bigWigLocation: bigDataLocation,
-                },
-            };
-        case 'vcfTabix':
-            return {
-                type: 'VariantTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'VcfTabixAdapter',
-                    vcfGzLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
-                    },
-                },
-            };
-        case 'hic':
-            return {
-                type: 'HicTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'HicAdapter',
-                    hicLocation: bigDataLocation,
-                },
-            };
-        // unsupported types
-        //     case 'peptideMapping':
-        //     case 'gvf':
-        //     case 'ld2':
-        //     case 'narrowPeak':
-        //     case 'wig':
-        //     case 'wigMaf':
-        //     case 'halSnake':
-        //     case 'bed':
-        //     case 'bed5FloatScore':
-        //     case 'bedGraph':
-        //     case 'bedRnaElements':
-        //     case 'broadPeak':
-        //     case 'coloredExon':
-        default:
-            return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType, categories);
-    }
-}
-var ucscAssemblies_1 = require("./ucscAssemblies");
-Object.defineProperty(exports, "ucscAssemblies", { enumerable: true, get: function () { return __importDefault(ucscAssemblies_1).default; } });

package/esm/ucsc-trackhub/index.js

@@ -1,13 +0,0 @@
-import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-import stateModelFactory from './model';
-import configSchema from './configSchema';
-export default function UCSCTrackHubConnectionF(pluginManager) {
-    pluginManager.addConnectionType(() => new ConnectionType({
-        name: 'UCSCTrackHubConnection',
-        configSchema,
-        stateModel: stateModelFactory(pluginManager),
-        displayName: 'UCSC Track Hub',
-        description: 'A track or assembly hub in the Track Hub format',
-        url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
-    }));
-}

package/esm/ucsc-trackhub/ucscTrackHub.js

@@ -1,195 +0,0 @@
-import { isUriLocation, notEmpty, objectHash, } from '@jbrowse/core/util';
-import { openLocation } from '@jbrowse/core/util/io';
-import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
-import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
-export async function fetchGenomesFile(genomesLoc) {
-    const genomesFileText = await openLocation(genomesLoc).readFile('utf8');
-    return new GenomesFile(genomesFileText);
-}
-export async function fetchTrackDbFile(trackDbLoc) {
-    const text = await openLocation(trackDbLoc).readFile('utf8');
-    return new TrackDbFile(text);
-}
-export function makeLoc(first, base) {
-    return {
-        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
-        locationType: 'UriLocation',
-    };
-}
-export function makeLocAlt(first, alt, base) {
-    return first ? makeLoc(first, base) : makeLoc(alt, base);
-}
-export function makeLoc2(first, alt) {
-    return first
-        ? {
-            uri: first,
-            locationType: 'LocalPath',
-        }
-        : {
-            uri: alt,
-            locationType: 'UriLocation',
-        };
-}
-export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }) {
-    return Object.entries(trackDb.data)
-        .map(([trackName, track]) => {
-        var _a;
-        const trackKeys = Object.keys(track);
-        const parentTrackKeys = new Set([
-            'superTrack',
-            'compositeTrack',
-            'container',
-            'view',
-        ]);
-        if (trackKeys.some(key => parentTrackKeys.has(key))) {
-            return undefined;
-        }
-        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();
-        const categories = parentTracks
-            .map(p => p === null || p === void 0 ? void 0 : p.data.shortLabel)
-            .filter((f) => !!f);
-        const res = makeTrackConfig({
-            track: track,
-            categories,
-            trackDbLoc,
-            trackDb,
-            sequenceAdapter,
-        });
-        return {
-            ...res,
-            trackId: `ucsc-trackhub-${objectHash(res)}`,
-            assemblyNames: [assemblyName],
-        };
-    })
-        .filter(notEmpty);
-}
-function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapter, }) {
-    var _a;
-    const trackType = track.data.type || ((_a = trackDb.data[track.data.parent || '']) === null || _a === void 0 ? void 0 : _a.data.type) || '';
-    const name = track.data.shortLabel || '';
-    const bigDataUrl = track.data.bigDataUrl || '';
-    const bigDataIdx = track.data.bigDataIndex || '';
-    const isUri = isUriLocation(trackDbLoc);
-    let baseTrackType = trackType.split(' ')[0] || '';
-    if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
-        baseTrackType = 'cram';
-    }
-    const bigDataLocation = isUri
-        ? makeLoc(bigDataUrl, trackDbLoc)
-        : makeLoc2(bigDataUrl);
-    switch (baseTrackType) {
-        case 'bam':
-            return {
-                type: 'AlignmentsTrack',
-                name: track.data.longLabel,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BamAdapter',
-                    bamLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
-                    },
-                },
-            };
-        case 'cram':
-            return {
-                type: 'AlignmentsTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'CramAdapter',
-                    cramLocation: bigDataLocation,
-                    craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
-                        : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
-                    sequenceAdapter,
-                },
-            };
-        case 'bigBarChart':
-        case 'bigBed':
-        case 'bigGenePred':
-        case 'bigChain':
-        case 'bigInteract':
-        case 'bigMaf':
-        case 'bigNarrowPeak':
-        case 'bigPsl':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
-        case 'bigWig':
-            return {
-                type: 'QuantitativeTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigWigAdapter',
-                    bigWigLocation: bigDataLocation,
-                },
-            };
-        case 'vcfTabix':
-            return {
-                type: 'VariantTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'VcfTabixAdapter',
-                    vcfGzLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
-                    },
-                },
-            };
-        case 'hic':
-            return {
-                type: 'HicTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'HicAdapter',
-                    hicLocation: bigDataLocation,
-                },
-            };
-        // unsupported types
-        //     case 'peptideMapping':
-        //     case 'gvf':
-        //     case 'ld2':
-        //     case 'narrowPeak':
-        //     case 'wig':
-        //     case 'wigMaf':
-        //     case 'halSnake':
-        //     case 'bed':
-        //     case 'bed5FloatScore':
-        //     case 'bedGraph':
-        //     case 'bedRnaElements':
-        //     case 'broadPeak':
-        //     case 'coloredExon':
-        default:
-            return generateUnknownTrackConf(name, baseTrackType, categories);
-    }
-}
-export { default as ucscAssemblies } from './ucscAssemblies';