jbrowse2: x/static/js/8435.484d30f8.chunk.js.map comparison

comparison x/static/js/8435.484d30f8.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

author	fubar
date	Sat, 05 Oct 2024 23:58:05 +0000
parents
children

comparison

equal deleted inserted replaced

124:137e08517410	125:49f3d3878413
	1 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Class representing an ra file stanza. Each stanza line is split into its key\n * and value and stored as a Map, so the usual Map methods can be used on the\n * stanza.\n /\nexport default class RaStanza {\n data: Record<string, string> = {}\n\n name?: string\n\n nameKey?: string\n\n constructor(\n stanza: string \| string[] = [],\n options?: { checkIndent?: boolean; skipValidation?: boolean },\n ) {\n const { checkIndent = true, skipValidation = false } = options ?? {}\n let stanzaLines: string[]\n if (typeof stanza === 'string') {\n stanzaLines = stanza.trimEnd().split(/\\r?\\n/)\n } else if (stanza) {\n stanzaLines = stanza\n } else {\n stanzaLines = []\n }\n\n let currentIndent: string \| undefined\n\n let continuedLine: string \| undefined\n for (const line of stanzaLines) {\n if (line === '') {\n throw new Error('Invalid stanza, contained blank lines')\n }\n if (line.trim().startsWith('#')) {\n continue\n }\n if (line.trimEnd().endsWith('\\\\')) {\n const trimmedLine = line.trimEnd().slice(0, -1)\n if (continuedLine) {\n continuedLine += trimmedLine.trimStart()\n } else {\n continuedLine = trimmedLine\n }\n continue\n }\n let combinedLine = line\n if (continuedLine) {\n combinedLine = continuedLine + combinedLine.trimStart()\n continuedLine = undefined\n }\n if (currentIndent ?? checkIndent) {\n const indent = combinedLine.match(/^([ \\t]+)/)\n if (currentIndent === undefined) {\n if (indent) {\n ;[, currentIndent] = indent\n } else {\n currentIndent = ''\n }\n } else if (\n (currentIndent === '' && indent !== null) \|\|\n (currentIndent && indent && currentIndent !== indent[1])\n ) {\n throw new Error('Inconsistent indentation of stanza')\n }\n } else {\n currentIndent = ''\n }\n const trimmedLine = combinedLine.trim()\n const sep = trimmedLine.indexOf(' ')\n if (sep === -1) {\n if (!this.nameKey) {\n throw new Error(\n 'First line in a stanza must have both a key and a value',\n )\n }\n // Adding a key that already exists and has no value is a no-op\n if (this.data[trimmedLine]) {\n continue\n }\n this.data[trimmedLine] = ''\n continue\n }\n const key = trimmedLine.slice(0, sep)\n const value = trimmedLine.slice(sep + 1)\n if (this.data[key] && value !== this.data[key]) {\n throw new Error(\n 'Got duplicate key with a different value in stanza: ' +\n `\"${key}\" key has both ${this.data[key]} and ${value}`,\n )\n }\n if (!this.nameKey) {\n this.nameKey = key\n this.name = trimmedLine.slice(sep + 1)\n }\n this.data[key] = value\n }\n\n if (!skipValidation) {\n this.validate()\n }\n }\n\n protected validate() {}\n}\n","import RaStanza from './raStanza'\n\n/\n Class representing an ra file. Each file is composed of multiple stanzas, and\n * each stanza is separated by one or more blank lines. Each stanza is stored in\n * a Map with the key being the value of the first key-value pair in the stanza.\n * The usual Map methods can be used on the file. An additional method `add()`\n * is available to take a raw line of text and break it up into a key and value\n * and add them to the class. This should be favored over `set()` when possible,\n * as it performs more validity checks than using `set()`.\n * @extends Map\n * @property {undefined\|string} nameKey - The key of the first line of all the\n * stanzas (`undefined` if the stanza has no lines yet).\n * @throws {Error} Throws if an empty stanza is added, if the key in the first\n * key-value pair of each stanze isn't the same, or if two stanzas have the same\n * value for the key-value pair in their first lines.\n * @param {(string\|string[])} [raFile=[]] - An ra file, either as a single\n * string or an array of strings with one stanza per entry. Supports both LF\n * and CRLF line terminators.\n * @param {object} options\n * @param {boolean} options.checkIndent [true] - Check if a the stanzas within\n * the file are indented consistently and keep track of the indentation\n /\nexport default class RaFile {\n data: Record<string, RaStanza \| undefined> = {}\n\n nameKey?: string\n\n constructor(\n raFile: string \| string[] = [],\n options?: { checkIndent?: boolean; skipValidation?: boolean },\n ) {\n const { checkIndent = true, skipValidation = false } = options ?? {}\n let stanzas: string[]\n if (typeof raFile === 'string') {\n stanzas = raFile.trimEnd().split(/(?:[\\t ]\\r?\\n){2,}/)\n } else if (raFile) {\n stanzas = raFile\n } else {\n stanzas = []\n }\n for (const stanza of stanzas) {\n if (stanza === '') {\n throw new Error('Invalid stanza, was empty')\n }\n if (stanza.trim().startsWith('#')) {\n const stanzaLines = stanza\n .trimEnd()\n .split(/\\r?\\n/)\n .map(line => line.trim())\n if (stanzaLines.every(line => line.startsWith('#'))) {\n continue\n }\n }\n const raStanza = new RaStanza(stanza, { checkIndent })\n if (!this.nameKey) {\n this.nameKey = raStanza.nameKey\n } else if (raStanza.nameKey !== this.nameKey) {\n throw new Error(\n 'The first line in each stanza must have the same key. ' +\n `Saw both ${this.nameKey} and ${raStanza.nameKey}`,\n )\n }\n if (!raStanza.name) {\n throw new Error(`No stanza name: ${raStanza.name}`)\n }\n if (this.data[raStanza.name]) {\n throw new Error(`Got duplicate stanza name: ${raStanza.name}`)\n }\n\n this.data[raStanza.name] = raStanza\n }\n\n if (!skipValidation) {\n this.validate()\n }\n }\n\n protected validate() {}\n}\n","import RaStanza from './raStanza'\n\n// validate that all required fields are present in the map\nexport function validateRequiredFieldsArePresent(\n map: RaStanza,\n requiredFields: string[],\n description = '',\n) {\n const missingFields: string[] = []\n for (const field of requiredFields) {\n if (!map.data[field]) {\n missingFields.push(field)\n }\n }\n if (missingFields.length > 0) {\n throw new Error(\n `${description} is missing required entr${\n missingFields.length === 1 ? 'y' : 'ies'\n }: ${missingFields.join(', ')}`,\n )\n }\n}\n","import RaFile from './raFile'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/*\n Class representing a genomes.txt file.\n * @extends RaFile\n * @param {(string\|string[])} [trackDbFile=[]] - A trackDb.txt file as a string\n * @throws {Error} Throws if \"track\" is not the first key in each track or if a\n * track is missing required keys\n /\nexport default class TrackDbFile extends RaFile {\n constructor(\n trackDbFile: string,\n options?: ConstructorParameters<typeof RaFile>[1],\n ) {\n super(trackDbFile, { ...options, checkIndent: false })\n }\n\n protected validate() {\n if (this.nameKey !== 'track') {\n throw new Error(\n `trackDb has \"${this.nameKey}\" instead of \"track\" as the first line in each track`,\n )\n }\n for (const [trackName, track] of Object.entries(this.data)) {\n const trackKeys = Object.keys(track!.data)\n validateRequiredFieldsArePresent(\n track!,\n ['track', 'shortLabel'],\n `Track ${trackName}`,\n )\n\n const parentTrackKeys = new Set([\n 'superTrack',\n 'compositeTrack',\n 'container',\n 'view',\n ])\n if (!trackKeys.some(key => parentTrackKeys.has(key))) {\n if (!trackKeys.includes('bigDataUrl')) {\n throw new Error(\n `Track ${trackName} is missing required key \"bigDataUrl\"`,\n )\n }\n if (!trackKeys.includes('type')) {\n const settingsKeys = Object.keys(this.settings(trackName))\n if (!settingsKeys.includes('type')) {\n throw new Error(\n `Neither track ${trackName} nor any of its parent tracks have the required key \"type\"`,\n )\n }\n }\n }\n let currentTrackName: string \| undefined = trackName\n do {\n // @ts-expect-error\n currentTrackName = this.data[currentTrackName]?.parent as\n \| string\n \| undefined\n if (currentTrackName) {\n ;[currentTrackName] = currentTrackName.split(' ')\n }\n } while (currentTrackName)\n const currentTrack = this.data[trackName]\n if (currentTrack) {\n this.data[trackName] = currentTrack\n }\n }\n }\n\n /\n Gets all track entries including those of parent tracks, with closer\n * entries overriding more distant ones\n * @param {string} trackName The name of a track\n * @throws {Error} Throws if track name does not exist in the trackDb\n /\n settings(trackName: string) {\n if (!this.data[trackName]) {\n throw new Error(`Track ${trackName} does not exist`)\n }\n const parentTracks = [trackName]\n let currentTrackName: string \| undefined = trackName\n do {\n // @ts-expect-error\n currentTrackName = this.data[currentTrackName]?.parent as\n \| string\n \| undefined\n if (currentTrackName) {\n parentTracks.push(currentTrackName)\n }\n } while (currentTrackName)\n const settings = {} as Record<string, unknown>\n parentTracks.reverse()\n for (const parentTrack of parentTracks) {\n const ret = this.data[parentTrack]\n if (ret) {\n for (const [key, value] of Object.entries(ret)) {\n settings[key] = value\n }\n }\n }\n return settings\n }\n}\n","import RaFile from './raFile'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/\n Class representing a genomes.txt file.\n * @extends RaFile\n * @param {(string\|string[])} [genomesFile=[]] - A genomes.txt file as a string\n * @throws {Error} Throws if the first line of the hub.txt file doesn't start\n * with \"genome <genome_name>\" or if it has invalid entries\n /\nexport default class GenomesFile extends RaFile {\n public validate(requiredFields = ['genome', 'trackDb']) {\n // TODO: check if genome is hosted by UCSC and if not, require twoBitPath and groups\n\n if (this.nameKey !== 'genome') {\n throw new Error(\n 'Genomes file must begin with a line like \"genome <genome_name>\"',\n )\n }\n\n for (const [genomeName, genome] of Object.entries(this.data)) {\n validateRequiredFieldsArePresent(\n genome!,\n requiredFields,\n `genome ${genomeName}`,\n )\n }\n }\n}\n","import RaStanza from './raStanza'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/\n Class representing a hub.txt file.\n * @extends RaStanza\n * @param {(string\|string[])} [hubFile=[]] - A hub.txt file as a string\n * @throws {Error} Throws if the first line of the hub.txt file doesn't start\n * with \"hub <hub_name>\", if it has invalid entries, or is missing required\n * entries\n /\nexport default class HubFile extends RaStanza {\n protected validate() {\n validateRequiredFieldsArePresent(\n this,\n ['hub', 'shortLabel', 'longLabel', 'genomesFile', 'email'],\n 'Hub file',\n )\n }\n}\n","import RaStanza from './raStanza'\nimport TrackDbFile from './trackDbFile'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/\n Class representing a \"single-file\" hub.txt file that contains all the\n * sections of a hub in a single file.\n /\nexport default class SingleFileHub {\n public genome: RaStanza\n\n public tracks: TrackDbFile\n\n public hubData: RaStanza\n\n constructor(hubText: string) {\n const [hubSection, genomeSection, ...trackSections] = hubText\n .trimEnd()\n .split(/(?:[\\t ]\\r?\\n){2,}/)\n this.hubData = new RaStanza(hubSection)\n this.validateHub()\n\n this.genome = new RaStanza(genomeSection)\n this.validateGenomeSection()\n\n this.tracks = new TrackDbFile(trackSections.join('\\n\\n'), {\n skipValidation: false,\n })\n }\n\n protected validateHub() {\n if (this.hubData.nameKey !== 'hub') {\n throw new Error('Hub file must begin with a line like \"hub <hub_name>\"')\n }\n\n validateRequiredFieldsArePresent(this.hubData, [\n 'hub',\n 'shortLabel',\n 'longLabel',\n 'email',\n 'descriptionUrl',\n ])\n }\n\n protected validateGenomeSection() {\n if (this.genome.nameKey !== 'genome') {\n throw new Error(\n 'Genomes file must begin with a line like \"genome <genome_name>\"',\n )\n }\n }\n}\n","import {\n FileLocation,\n isUriLocation,\n notEmpty,\n objectHash,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { generateUnknownTrackConf } from '@jbrowse/core/util/tracks'\nimport { RaStanza, GenomesFile, TrackDbFile } from '@gmod/ucsc-hub'\n\nexport async function fetchGenomesFile(genomesLoc: FileLocation) {\n const genomesFileText = await openLocation(genomesLoc).readFile('utf8')\n return new GenomesFile(genomesFileText)\n}\n\nexport async function fetchTrackDbFile(trackDbLoc: FileLocation) {\n const text = await openLocation(trackDbLoc).readFile('utf8')\n return new TrackDbFile(text)\n}\n\nexport function makeLoc(\n first: string,\n base: { uri: string; baseUri?: string },\n) {\n return {\n uri: new URL(first, new URL(base.uri, base.baseUri)).href,\n locationType: 'UriLocation',\n }\n}\n\nexport function makeLocAlt(first: string, alt: string, base: { uri: string }) {\n return first ? makeLoc(first, base) : makeLoc(alt, base)\n}\n\nexport function makeLoc2(first: string, alt?: string) {\n return first\n ? {\n uri: first,\n locationType: 'LocalPath',\n }\n : {\n uri: alt,\n locationType: 'UriLocation',\n }\n}\n\nexport function generateTracks({\n trackDb,\n trackDbLoc,\n assemblyName,\n sequenceAdapter,\n}: {\n trackDb: TrackDbFile\n trackDbLoc: FileLocation\n assemblyName: string\n sequenceAdapter: any\n}) {\n return Object.entries(trackDb.data)\n .map(([trackName, track]) => {\n const trackKeys = Object.keys(track!)\n const parentTrackKeys = new Set([\n 'superTrack',\n 'compositeTrack',\n 'container',\n 'view',\n ])\n if (trackKeys.some(key => parentTrackKeys.has(key))) {\n return undefined\n }\n const parentTracks = []\n let currentTrackName = trackName\n do {\n currentTrackName = trackDb.data[currentTrackName]?.data.parent \|\| ''\n if (currentTrackName) {\n currentTrackName = currentTrackName.split(' ')[0]!\n parentTracks.push(trackDb.data[currentTrackName])\n }\n } while (currentTrackName)\n parentTracks.reverse()\n const categories = parentTracks\n .map(p => p?.data.shortLabel)\n .filter((f): f is string => !!f)\n const res = makeTrackConfig({\n track: track!,\n categories,\n trackDbLoc,\n trackDb,\n sequenceAdapter,\n })\n return {\n ...res,\n trackId: `ucsc-trackhub-${objectHash(res)}`,\n assemblyNames: [assemblyName],\n }\n })\n .filter(notEmpty)\n}\n\nfunction makeTrackConfig({\n track,\n categories,\n trackDbLoc,\n trackDb,\n sequenceAdapter,\n}: {\n track: RaStanza\n categories: string[]\n trackDbLoc: FileLocation\n trackDb: TrackDbFile\n sequenceAdapter: any\n}) {\n const trackType =\n track.data.type \|\| trackDb.data[track.data.parent \|\| '']?.data.type \|\| ''\n const name = track.data.shortLabel \|\| ''\n const bigDataUrl = track.data.bigDataUrl \|\| ''\n const bigDataIdx = track.data.bigDataIndex \|\| ''\n const isUri = isUriLocation(trackDbLoc)\n let baseTrackType = trackType.split(' ')[0] \|\| ''\n if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {\n baseTrackType = 'cram'\n }\n const bigDataLocation = isUri\n ? makeLoc(bigDataUrl, trackDbLoc)\n : makeLoc2(bigDataUrl)\n\n switch (baseTrackType) {\n case 'bam':\n return {\n type: 'AlignmentsTrack',\n name: track.data.longLabel,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'BamAdapter',\n bamLocation: bigDataLocation,\n index: {\n location: isUri\n ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)\n : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),\n },\n },\n }\n\n case 'cram':\n return {\n type: 'AlignmentsTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'CramAdapter',\n cramLocation: bigDataLocation,\n craiLocation: isUri\n ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)\n : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),\n sequenceAdapter,\n },\n }\n case 'bigBarChart':\n case 'bigBed':\n case 'bigGenePred':\n case 'bigChain':\n case 'bigInteract':\n case 'bigMaf':\n case 'bigNarrowPeak':\n case 'bigPsl':\n return {\n type: 'FeatureTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'BigBedAdapter',\n bigBedLocation: bigDataLocation,\n },\n }\n case 'bigWig':\n return {\n type: 'QuantitativeTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'BigWigAdapter',\n bigWigLocation: bigDataLocation,\n },\n }\n\n case 'vcfTabix':\n return {\n type: 'VariantTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'VcfTabixAdapter',\n vcfGzLocation: bigDataLocation,\n index: {\n location: isUri\n ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)\n : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),\n },\n },\n }\n\n case 'hic':\n return {\n type: 'HicTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'HicAdapter',\n hicLocation: bigDataLocation,\n },\n }\n\n // unsupported types\n // case 'peptideMapping':\n // case 'gvf':\n // case 'ld2':\n // case 'narrowPeak':\n // case 'wig':\n // case 'wigMaf':\n // case 'halSnake':\n // case 'bed':\n // case 'bed5FloatScore':\n // case 'bedGraph':\n // case 'bedRnaElements':\n // case 'broadPeak':\n // case 'coloredExon':\n default:\n return generateUnknownTrackConf(name, baseTrackType, categories)\n }\n}\n\nexport { default as ucscAssemblies } from './ucscAssemblies'\n","// These are the assemblies for which there is a sequence file located at\n// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit\n// This list was generated by `getUcscAssemblies.js`\n\nexport default `ailMel1\nallMis1\nanoCar1\nanoCar2\nanoGam1\nanoGam3\napiMel1\napiMel2\naplCal1\naptMan1\naquChr2\nbalAcu1\nbisBis1\nbosTau2\nbosTau3\nbosTau4\nbosTau6\nbosTau7\nbosTau8\nbraFlo1\ncaeJap1\ncaePb1\ncaePb2\ncaeRem2\ncaeRem3\ncalJac1\ncalJac3\ncalMil1\ncanFam1\ncanFam3\ncavPor3\ncb3\nce10\nce11\nce2\nce4\nce6\ncerSim1\nchlSab2\nchoHof1\nchrPic1\nci1\nci2\nci3\ncriGri1\ncriGriChoV1\ndanRer10\ndanRer11\ndanRer3\ndanRer4\ndanRer5\ndanRer6\ndanRer7\ndasNov3\ndipOrd1\ndm1\ndm2\ndm3\ndm6\ndp2\ndp3\ndroAna1\ndroAna2\ndroEre1\ndroGri1\ndroMoj1\ndroMoj2\ndroPer1\ndroSec1\ndroSim1\ndroVir1\ndroVir2\ndroYak1\ndroYak2\neboVir3\nechTel1\nechTel2\nequCab1\nequCab2\neriEur1\neriEur2\nfelCat3\nfelCat4\nfelCat5\nfelCat8\nfr1\nfr2\nfr3\ngadMor1\ngalGal2\ngalGal3\ngalGal4\ngalGal5\ngalGal6\ngalVar1\ngasAcu1\ngeoFor1\ngorGor3\ngorGor4\ngorGor5\nhetGla1\nhetGla2\nhg16\nhg18\nhg19\nhg38\nlatCha1\nloxAfr3\nmacEug2\nmacFas5\nmanPen1\nmelGal1\nmelGal5\nmelUnd1\nmicMur1\nmicMur2\nmm10\nmm7\nmm8\nmm9\nmonDom2\nmonDom4\nmonDom5\nmusFur1\nmyoLuc2\nnanPar1\nnasLar1\nnomLeu1\nnomLeu2\nnomLeu3\nochPri2\nochPri3\noreNil2\nornAna1\nornAna2\noryCun2\noryLat2\notoGar3\noviAri1\noviAri3\noviAri4\npanPan1\npanPan2\npanTro1\npanTro2\npanTro3\npanTro4\npanTro5\npanTro6\npapAnu2\npapHam1\npetMar1\npetMar2\nponAbe2\nponAbe3\npriPac1\nproCap1\npteVam1\nrheMac2\nrheMac3\nrheMac8\nrhiRox1\nrn4\nrn5\nrn6\nsacCer1\nsacCer2\nsacCer3\nsaiBol1\nsarHar1\nsorAra1\nsorAra2\nspeTri2\nstrPur1\nstrPur2\nsusScr11\nsusScr2\nsusScr3\ntaeGut1\ntaeGut2\ntarSyr1\ntarSyr2\ntetNig1\ntetNig2\nthaSir1\ntriMan1\ntupBel1\nturTru2\nventer1\nvicPac1\nvicPac2\nxenLae2\nxenTro1\nxenTro2\nxenTro3\nxenTro7\nxenTro9`.split(/\\r?\\n/)\n","import { HubFile, SingleFileHub } from '@gmod/ucsc-hub'\nimport {\n generateTracks,\n fetchGenomesFile,\n fetchTrackDbFile,\n} from './ucscTrackHub'\n\nimport { AnyConfigurationModel, getConf } from '@jbrowse/core/configuration'\nimport { FileLocation, getSession } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { nanoid } from '@jbrowse/core/util/nanoid'\n\nfunction resolve(uri: string, baseUri: string) {\n return new URL(uri, baseUri).href\n}\n\nexport async function doConnect(self: {\n configuration: AnyConfigurationModel\n addTrackConfs: (arg: Record<string, unknown>[]) => void\n}) {\n const session = getSession(self)\n const notLoadedAssemblies = [] as string[]\n try {\n const hubFileLocation = getConf(self, 'hubTxtLocation') as FileLocation\n const hubFileText = await openLocation(hubFileLocation).readFile('utf8')\n // @ts-expect-error\n const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri)\n const { assemblyManager } = session\n if (hubFileText.includes('useOneFile on')) {\n const hub = new SingleFileHub(hubFileText)\n const { genome, tracks } = hub\n const genomeName = genome.name!\n\n const asm = assemblyManager.get(genomeName)\n if (!asm) {\n // @ts-expect-error\n session.addSessionAssembly({\n name: genomeName,\n sequence: {\n type: 'ReferenceSequenceTrack',\n trackId: `${genomeName}-${nanoid()}`,\n adapter: {\n type: 'TwoBitAdapter',\n twoBitLocation: {\n uri: resolve(genome.data.twoBitPath!, hubUri),\n },\n chromSizesLocation: {\n uri: resolve(genome.data.chromSizes!, hubUri),\n },\n },\n },\n })\n }\n const asm2 = assemblyManager.get(genomeName)\n const sequenceAdapter = getConf(asm2!, ['sequence', 'adapter'])\n const tracksNew = generateTracks({\n trackDb: tracks,\n trackDbLoc: hubFileLocation,\n assemblyName: genomeName,\n sequenceAdapter,\n })\n self.addTrackConfs(tracksNew)\n } else {\n const hubFile = new HubFile(hubFileText)\n const genomeFile = hubFile.data.genomesFile\n if (!genomeFile) {\n throw new Error('genomesFile not found on hub')\n }\n\n // @ts-expect-error\n const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri)\n const genomesFileLocation = hubUri\n ? {\n uri: resolve(genomeFile, hubUri),\n locationType: 'UriLocation' as const,\n }\n : {\n localPath: genomeFile,\n locationType: 'LocalPathLocation' as const,\n }\n const genomesFile = await fetchGenomesFile(genomesFileLocation)\n const map = {} as Record<string, number>\n for (const [genomeName, genome] of Object.entries(genomesFile.data)) {\n const assemblyNames = getConf(self, 'assemblyNames')\n if (assemblyNames.length > 0 && !assemblyNames.includes(genomeName)) {\n continue\n }\n\n const asm = assemblyManager.get(genomeName)\n if (!asm) {\n notLoadedAssemblies.push(genomeName)\n continue\n }\n\n // @ts-expect-error\n const db = genome.data.trackDb\n if (!db) {\n throw new Error('genomesFile not found on hub')\n }\n const base = new URL(genomeFile, hubUri)\n const loc = hubUri\n ? {\n uri: new URL(db, base).href,\n locationType: 'UriLocation' as const,\n }\n : {\n localPath: db,\n locationType: 'LocalPathLocation' as const,\n }\n const trackDb = await fetchTrackDbFile(loc)\n const sequenceAdapter = getConf(asm, ['sequence', 'adapter'])\n const tracks = generateTracks({\n trackDb,\n trackDbLoc: loc,\n assemblyName: genomeName,\n sequenceAdapter,\n })\n self.addTrackConfs(tracks)\n map[genomeName] = tracks.length\n }\n\n const loadedAssemblies = Object.entries(map)\n const str1 = loadedAssemblies.length\n ? `Loaded data from these assemblies: ${loadedAssemblies\n .map(([key, val]) => `${key} (${val} tracks)`)\n .join(', ')}`\n : ''\n const str2 = notLoadedAssemblies.length\n ? `Skipped data from these assemblies: ${notLoadedAssemblies.join(\n ', ',\n )}`\n : ''\n session.notify([str1, str2].filter(f => !!f).join('. '), 'success')\n }\n } catch (e) {\n console.error(e)\n session.notifyError(`${getConf(self, 'name')}: \"${e}\"`, e)\n session.breakConnection?.(self.configuration)\n }\n}\n"],"names":["RaStanza","constructor","stanza","options","data","checkIndent","skipValidation","stanzaLines","currentIndent","continuedLine","trimEnd","split","line","Error","trim","startsWith","endsWith","trimmedLine","slice","trimStart","combinedLine","undefined","indent","match","sep","indexOf","this","nameKey","key","value","name","validate","RaFile","raFile","stanzas","map","every","raStanza","validateRequiredFieldsArePresent","requiredFields","description","missingFields","field","push","length","join","TrackDbFile","trackDbFile","super","trackName","track","Object","entries","trackKeys","keys","parentTrackKeys","Set","some","has","includes","settings","currentTrackName","parent","currentTrack","parentTracks","reverse","parentTrack","ret","GenomesFile","genomeName","genome","HubFile","SingleFileHub","hubText","hubSection","genomeSection","trackSections","hubData","validateHub","validateGenomeSection","tracks","async","fetchTrackDbFile","trackDbLoc","text","openLocation","readFile","makeLoc","first","base","uri","URL","baseUri","href","locationType","makeLocAlt","alt","makeLoc2","generateTracks","trackDb","assemblyName","sequenceAdapter","res","categories","trackType","type","shortLabel","bigDataUrl","bigDataIdx","bigDataIndex","isUri","isUriLocation","baseTrackType","toLowerCase","bigDataLocation","longLabel","category","adapter","bamLocation","index","location","cramLocation","craiLocation","bigBedLocation","bigWigLocation","vcfGzLocation","hicLocation","generateUnknownTrackConf","makeTrackConfig","p","filter","f","trackId","objectHash","assemblyNames","notEmpty","resolve","doConnect","self","session","getSession","notLoadedAssemblies","hubFileLocation","getConf","hubFileText","hubUri","assemblyManager","hub","get","addSessionAssembly","sequence","nanoid","twoBitLocation","twoBitPath","chromSizesLocation","chromSizes","asm2","tracksNew","addTrackConfs","genomeFile","genomesFile","genomesFileLocation","localPath","genomesLoc","genomesFileText","fetchGenomesFile","asm","db","loc","loadedAssemblies","str1","val","str2","notify","e","console","error","notifyError","breakConnection","configuration"],"sourceRoot":""}

1 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* Class representing an ra file stanza. Each stanza line is split into its key\n * and value and stored as a Map, so the usual Map methods can be used on the\n * stanza.\n */\nexport default class RaStanza {\n data: Record<string, string> = {}\n\n name?: string\n\n nameKey?: string\n\n constructor(\n stanza: string | string[] = [],\n options?: { checkIndent?: boolean; skipValidation?: boolean },\n ) {\n const { checkIndent = true, skipValidation = false } = options ?? {}\n let stanzaLines: string[]\n if (typeof stanza === 'string') {\n stanzaLines = stanza.trimEnd().split(/\\r?\\n/)\n } else if (stanza) {\n stanzaLines = stanza\n } else {\n stanzaLines = []\n }\n\n let currentIndent: string | undefined\n\n let continuedLine: string | undefined\n for (const line of stanzaLines) {\n if (line === '') {\n throw new Error('Invalid stanza, contained blank lines')\n }\n if (line.trim().startsWith('#')) {\n continue\n }\n if (line.trimEnd().endsWith('\\\\')) {\n const trimmedLine = line.trimEnd().slice(0, -1)\n if (continuedLine) {\n continuedLine += trimmedLine.trimStart()\n } else {\n continuedLine = trimmedLine\n }\n continue\n }\n let combinedLine = line\n if (continuedLine) {\n combinedLine = continuedLine + combinedLine.trimStart()\n continuedLine = undefined\n }\n if (currentIndent ?? checkIndent) {\n const indent = combinedLine.match(/^([ \\t]+)/)\n if (currentIndent === undefined) {\n if (indent) {\n ;[, currentIndent] = indent\n } else {\n currentIndent = ''\n }\n } else if (\n (currentIndent === '' && indent !== null) ||\n (currentIndent && indent && currentIndent !== indent[1])\n ) {\n throw new Error('Inconsistent indentation of stanza')\n }\n } else {\n currentIndent = ''\n }\n const trimmedLine = combinedLine.trim()\n const sep = trimmedLine.indexOf(' ')\n if (sep === -1) {\n if (!this.nameKey) {\n throw new Error(\n 'First line in a stanza must have both a key and a value',\n )\n }\n // Adding a key that already exists and has no value is a no-op\n if (this.data[trimmedLine]) {\n continue\n }\n this.data[trimmedLine] = ''\n continue\n }\n const key = trimmedLine.slice(0, sep)\n const value = trimmedLine.slice(sep + 1)\n if (this.data[key] && value !== this.data[key]) {\n throw new Error(\n 'Got duplicate key with a different value in stanza: ' +\n `\"${key}\" key has both ${this.data[key]} and ${value}`,\n )\n }\n if (!this.nameKey) {\n this.nameKey = key\n this.name = trimmedLine.slice(sep + 1)\n }\n this.data[key] = value\n }\n\n if (!skipValidation) {\n this.validate()\n }\n }\n\n protected validate() {}\n}\n","import RaStanza from './raStanza'\n\n/**\n * Class representing an ra file. Each file is composed of multiple stanzas, and\n * each stanza is separated by one or more blank lines. Each stanza is stored in\n * a Map with the key being the value of the first key-value pair in the stanza.\n * The usual Map methods can be used on the file. An additional method `add()`\n * is available to take a raw line of text and break it up into a key and value\n * and add them to the class. This should be favored over `set()` when possible,\n * as it performs more validity checks than using `set()`.\n * @extends Map\n * @property {undefined|string} nameKey - The key of the first line of all the\n * stanzas (`undefined` if the stanza has no lines yet).\n * @throws {Error} Throws if an empty stanza is added, if the key in the first\n * key-value pair of each stanze isn't the same, or if two stanzas have the same\n * value for the key-value pair in their first lines.\n * @param {(string|string[])} [raFile=[]] - An ra file, either as a single\n * string or an array of strings with one stanza per entry. Supports both LF\n * and CRLF line terminators.\n * @param {object} options\n * @param {boolean} options.checkIndent [true] - Check if a the stanzas within\n * the file are indented consistently and keep track of the indentation\n */\nexport default class RaFile {\n data: Record<string, RaStanza | undefined> = {}\n\n nameKey?: string\n\n constructor(\n raFile: string | string[] = [],\n options?: { checkIndent?: boolean; skipValidation?: boolean },\n ) {\n const { checkIndent = true, skipValidation = false } = options ?? {}\n let stanzas: string[]\n if (typeof raFile === 'string') {\n stanzas = raFile.trimEnd().split(/(?:[\\t ]*\\r?\\n){2,}/)\n } else if (raFile) {\n stanzas = raFile\n } else {\n stanzas = []\n }\n for (const stanza of stanzas) {\n if (stanza === '') {\n throw new Error('Invalid stanza, was empty')\n }\n if (stanza.trim().startsWith('#')) {\n const stanzaLines = stanza\n .trimEnd()\n .split(/\\r?\\n/)\n .map(line => line.trim())\n if (stanzaLines.every(line => line.startsWith('#'))) {\n continue\n }\n }\n const raStanza = new RaStanza(stanza, { checkIndent })\n if (!this.nameKey) {\n this.nameKey = raStanza.nameKey\n } else if (raStanza.nameKey !== this.nameKey) {\n throw new Error(\n 'The first line in each stanza must have the same key. ' +\n `Saw both ${this.nameKey} and ${raStanza.nameKey}`,\n )\n }\n if (!raStanza.name) {\n throw new Error(`No stanza name: ${raStanza.name}`)\n }\n if (this.data[raStanza.name]) {\n throw new Error(`Got duplicate stanza name: ${raStanza.name}`)\n }\n\n this.data[raStanza.name] = raStanza\n }\n\n if (!skipValidation) {\n this.validate()\n }\n }\n\n protected validate() {}\n}\n","import RaStanza from './raStanza'\n\n// validate that all required fields are present in the map\nexport function validateRequiredFieldsArePresent(\n map: RaStanza,\n requiredFields: string[],\n description = '',\n) {\n const missingFields: string[] = []\n for (const field of requiredFields) {\n if (!map.data[field]) {\n missingFields.push(field)\n }\n }\n if (missingFields.length > 0) {\n throw new Error(\n `${description} is missing required entr${\n missingFields.length === 1 ? 'y' : 'ies'\n }: ${missingFields.join(', ')}`,\n )\n }\n}\n","import RaFile from './raFile'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/**\n * Class representing a genomes.txt file.\n * @extends RaFile\n * @param {(string|string[])} [trackDbFile=[]] - A trackDb.txt file as a string\n * @throws {Error} Throws if \"track\" is not the first key in each track or if a\n * track is missing required keys\n */\nexport default class TrackDbFile extends RaFile {\n constructor(\n trackDbFile: string,\n options?: ConstructorParameters<typeof RaFile>[1],\n ) {\n super(trackDbFile, { ...options, checkIndent: false })\n }\n\n protected validate() {\n if (this.nameKey !== 'track') {\n throw new Error(\n `trackDb has \"${this.nameKey}\" instead of \"track\" as the first line in each track`,\n )\n }\n for (const [trackName, track] of Object.entries(this.data)) {\n const trackKeys = Object.keys(track!.data)\n validateRequiredFieldsArePresent(\n track!,\n ['track', 'shortLabel'],\n `Track ${trackName}`,\n )\n\n const parentTrackKeys = new Set([\n 'superTrack',\n 'compositeTrack',\n 'container',\n 'view',\n ])\n if (!trackKeys.some(key => parentTrackKeys.has(key))) {\n if (!trackKeys.includes('bigDataUrl')) {\n throw new Error(\n `Track ${trackName} is missing required key \"bigDataUrl\"`,\n )\n }\n if (!trackKeys.includes('type')) {\n const settingsKeys = Object.keys(this.settings(trackName))\n if (!settingsKeys.includes('type')) {\n throw new Error(\n `Neither track ${trackName} nor any of its parent tracks have the required key \"type\"`,\n )\n }\n }\n }\n let currentTrackName: string | undefined = trackName\n do {\n // @ts-expect-error\n currentTrackName = this.data[currentTrackName]?.parent as\n | string\n | undefined\n if (currentTrackName) {\n ;[currentTrackName] = currentTrackName.split(' ')\n }\n } while (currentTrackName)\n const currentTrack = this.data[trackName]\n if (currentTrack) {\n this.data[trackName] = currentTrack\n }\n }\n }\n\n /**\n * Gets all track entries including those of parent tracks, with closer\n * entries overriding more distant ones\n * @param {string} trackName The name of a track\n * @throws {Error} Throws if track name does not exist in the trackDb\n */\n settings(trackName: string) {\n if (!this.data[trackName]) {\n throw new Error(`Track ${trackName} does not exist`)\n }\n const parentTracks = [trackName]\n let currentTrackName: string | undefined = trackName\n do {\n // @ts-expect-error\n currentTrackName = this.data[currentTrackName]?.parent as\n | string\n | undefined\n if (currentTrackName) {\n parentTracks.push(currentTrackName)\n }\n } while (currentTrackName)\n const settings = {} as Record<string, unknown>\n parentTracks.reverse()\n for (const parentTrack of parentTracks) {\n const ret = this.data[parentTrack]\n if (ret) {\n for (const [key, value] of Object.entries(ret)) {\n settings[key] = value\n }\n }\n }\n return settings\n }\n}\n","import RaFile from './raFile'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/**\n * Class representing a genomes.txt file.\n * @extends RaFile\n * @param {(string|string[])} [genomesFile=[]] - A genomes.txt file as a string\n * @throws {Error} Throws if the first line of the hub.txt file doesn't start\n * with \"genome <genome_name>\" or if it has invalid entries\n */\nexport default class GenomesFile extends RaFile {\n public validate(requiredFields = ['genome', 'trackDb']) {\n // TODO: check if genome is hosted by UCSC and if not, require twoBitPath and groups\n\n if (this.nameKey !== 'genome') {\n throw new Error(\n 'Genomes file must begin with a line like \"genome <genome_name>\"',\n )\n }\n\n for (const [genomeName, genome] of Object.entries(this.data)) {\n validateRequiredFieldsArePresent(\n genome!,\n requiredFields,\n `genome ${genomeName}`,\n )\n }\n }\n}\n","import RaStanza from './raStanza'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/**\n * Class representing a hub.txt file.\n * @extends RaStanza\n * @param {(string|string[])} [hubFile=[]] - A hub.txt file as a string\n * @throws {Error} Throws if the first line of the hub.txt file doesn't start\n * with \"hub <hub_name>\", if it has invalid entries, or is missing required\n * entries\n */\nexport default class HubFile extends RaStanza {\n protected validate() {\n validateRequiredFieldsArePresent(\n this,\n ['hub', 'shortLabel', 'longLabel', 'genomesFile', 'email'],\n 'Hub file',\n )\n }\n}\n","import RaStanza from './raStanza'\nimport TrackDbFile from './trackDbFile'\nimport { validateRequiredFieldsArePresent } from './util'\n\n/**\n * Class representing a \"single-file\" hub.txt file that contains all the\n * sections of a hub in a single file.\n */\nexport default class SingleFileHub {\n public genome: RaStanza\n\n public tracks: TrackDbFile\n\n public hubData: RaStanza\n\n constructor(hubText: string) {\n const [hubSection, genomeSection, ...trackSections] = hubText\n .trimEnd()\n .split(/(?:[\\t ]*\\r?\\n){2,}/)\n this.hubData = new RaStanza(hubSection)\n this.validateHub()\n\n this.genome = new RaStanza(genomeSection)\n this.validateGenomeSection()\n\n this.tracks = new TrackDbFile(trackSections.join('\\n\\n'), {\n skipValidation: false,\n })\n }\n\n protected validateHub() {\n if (this.hubData.nameKey !== 'hub') {\n throw new Error('Hub file must begin with a line like \"hub <hub_name>\"')\n }\n\n validateRequiredFieldsArePresent(this.hubData, [\n 'hub',\n 'shortLabel',\n 'longLabel',\n 'email',\n 'descriptionUrl',\n ])\n }\n\n protected validateGenomeSection() {\n if (this.genome.nameKey !== 'genome') {\n throw new Error(\n 'Genomes file must begin with a line like \"genome <genome_name>\"',\n )\n }\n }\n}\n","import {\n FileLocation,\n isUriLocation,\n notEmpty,\n objectHash,\n} from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { generateUnknownTrackConf } from '@jbrowse/core/util/tracks'\nimport { RaStanza, GenomesFile, TrackDbFile } from '@gmod/ucsc-hub'\n\nexport async function fetchGenomesFile(genomesLoc: FileLocation) {\n const genomesFileText = await openLocation(genomesLoc).readFile('utf8')\n return new GenomesFile(genomesFileText)\n}\n\nexport async function fetchTrackDbFile(trackDbLoc: FileLocation) {\n const text = await openLocation(trackDbLoc).readFile('utf8')\n return new TrackDbFile(text)\n}\n\nexport function makeLoc(\n first: string,\n base: { uri: string; baseUri?: string },\n) {\n return {\n uri: new URL(first, new URL(base.uri, base.baseUri)).href,\n locationType: 'UriLocation',\n }\n}\n\nexport function makeLocAlt(first: string, alt: string, base: { uri: string }) {\n return first ? makeLoc(first, base) : makeLoc(alt, base)\n}\n\nexport function makeLoc2(first: string, alt?: string) {\n return first\n ? {\n uri: first,\n locationType: 'LocalPath',\n }\n : {\n uri: alt,\n locationType: 'UriLocation',\n }\n}\n\nexport function generateTracks({\n trackDb,\n trackDbLoc,\n assemblyName,\n sequenceAdapter,\n}: {\n trackDb: TrackDbFile\n trackDbLoc: FileLocation\n assemblyName: string\n sequenceAdapter: any\n}) {\n return Object.entries(trackDb.data)\n .map(([trackName, track]) => {\n const trackKeys = Object.keys(track!)\n const parentTrackKeys = new Set([\n 'superTrack',\n 'compositeTrack',\n 'container',\n 'view',\n ])\n if (trackKeys.some(key => parentTrackKeys.has(key))) {\n return undefined\n }\n const parentTracks = []\n let currentTrackName = trackName\n do {\n currentTrackName = trackDb.data[currentTrackName]?.data.parent || ''\n if (currentTrackName) {\n currentTrackName = currentTrackName.split(' ')[0]!\n parentTracks.push(trackDb.data[currentTrackName])\n }\n } while (currentTrackName)\n parentTracks.reverse()\n const categories = parentTracks\n .map(p => p?.data.shortLabel)\n .filter((f): f is string => !!f)\n const res = makeTrackConfig({\n track: track!,\n categories,\n trackDbLoc,\n trackDb,\n sequenceAdapter,\n })\n return {\n ...res,\n trackId: `ucsc-trackhub-${objectHash(res)}`,\n assemblyNames: [assemblyName],\n }\n })\n .filter(notEmpty)\n}\n\nfunction makeTrackConfig({\n track,\n categories,\n trackDbLoc,\n trackDb,\n sequenceAdapter,\n}: {\n track: RaStanza\n categories: string[]\n trackDbLoc: FileLocation\n trackDb: TrackDbFile\n sequenceAdapter: any\n}) {\n const trackType =\n track.data.type || trackDb.data[track.data.parent || '']?.data.type || ''\n const name = track.data.shortLabel || ''\n const bigDataUrl = track.data.bigDataUrl || ''\n const bigDataIdx = track.data.bigDataIndex || ''\n const isUri = isUriLocation(trackDbLoc)\n let baseTrackType = trackType.split(' ')[0] || ''\n if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {\n baseTrackType = 'cram'\n }\n const bigDataLocation = isUri\n ? makeLoc(bigDataUrl, trackDbLoc)\n : makeLoc2(bigDataUrl)\n\n switch (baseTrackType) {\n case 'bam':\n return {\n type: 'AlignmentsTrack',\n name: track.data.longLabel,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'BamAdapter',\n bamLocation: bigDataLocation,\n index: {\n location: isUri\n ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)\n : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),\n },\n },\n }\n\n case 'cram':\n return {\n type: 'AlignmentsTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'CramAdapter',\n cramLocation: bigDataLocation,\n craiLocation: isUri\n ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)\n : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),\n sequenceAdapter,\n },\n }\n case 'bigBarChart':\n case 'bigBed':\n case 'bigGenePred':\n case 'bigChain':\n case 'bigInteract':\n case 'bigMaf':\n case 'bigNarrowPeak':\n case 'bigPsl':\n return {\n type: 'FeatureTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'BigBedAdapter',\n bigBedLocation: bigDataLocation,\n },\n }\n case 'bigWig':\n return {\n type: 'QuantitativeTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'BigWigAdapter',\n bigWigLocation: bigDataLocation,\n },\n }\n\n case 'vcfTabix':\n return {\n type: 'VariantTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'VcfTabixAdapter',\n vcfGzLocation: bigDataLocation,\n index: {\n location: isUri\n ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)\n : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),\n },\n },\n }\n\n case 'hic':\n return {\n type: 'HicTrack',\n name,\n description: track.data.longLabel,\n category: categories,\n adapter: {\n type: 'HicAdapter',\n hicLocation: bigDataLocation,\n },\n }\n\n // unsupported types\n // case 'peptideMapping':\n // case 'gvf':\n // case 'ld2':\n // case 'narrowPeak':\n // case 'wig':\n // case 'wigMaf':\n // case 'halSnake':\n // case 'bed':\n // case 'bed5FloatScore':\n // case 'bedGraph':\n // case 'bedRnaElements':\n // case 'broadPeak':\n // case 'coloredExon':\n default:\n return generateUnknownTrackConf(name, baseTrackType, categories)\n }\n}\n\nexport { default as ucscAssemblies } from './ucscAssemblies'\n","// These are the assemblies for which there is a sequence file located at\n// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit\n// This list was generated by `getUcscAssemblies.js`\n\nexport default `ailMel1\nallMis1\nanoCar1\nanoCar2\nanoGam1\nanoGam3\napiMel1\napiMel2\naplCal1\naptMan1\naquChr2\nbalAcu1\nbisBis1\nbosTau2\nbosTau3\nbosTau4\nbosTau6\nbosTau7\nbosTau8\nbraFlo1\ncaeJap1\ncaePb1\ncaePb2\ncaeRem2\ncaeRem3\ncalJac1\ncalJac3\ncalMil1\ncanFam1\ncanFam3\ncavPor3\ncb3\nce10\nce11\nce2\nce4\nce6\ncerSim1\nchlSab2\nchoHof1\nchrPic1\nci1\nci2\nci3\ncriGri1\ncriGriChoV1\ndanRer10\ndanRer11\ndanRer3\ndanRer4\ndanRer5\ndanRer6\ndanRer7\ndasNov3\ndipOrd1\ndm1\ndm2\ndm3\ndm6\ndp2\ndp3\ndroAna1\ndroAna2\ndroEre1\ndroGri1\ndroMoj1\ndroMoj2\ndroPer1\ndroSec1\ndroSim1\ndroVir1\ndroVir2\ndroYak1\ndroYak2\neboVir3\nechTel1\nechTel2\nequCab1\nequCab2\neriEur1\neriEur2\nfelCat3\nfelCat4\nfelCat5\nfelCat8\nfr1\nfr2\nfr3\ngadMor1\ngalGal2\ngalGal3\ngalGal4\ngalGal5\ngalGal6\ngalVar1\ngasAcu1\ngeoFor1\ngorGor3\ngorGor4\ngorGor5\nhetGla1\nhetGla2\nhg16\nhg18\nhg19\nhg38\nlatCha1\nloxAfr3\nmacEug2\nmacFas5\nmanPen1\nmelGal1\nmelGal5\nmelUnd1\nmicMur1\nmicMur2\nmm10\nmm7\nmm8\nmm9\nmonDom2\nmonDom4\nmonDom5\nmusFur1\nmyoLuc2\nnanPar1\nnasLar1\nnomLeu1\nnomLeu2\nnomLeu3\nochPri2\nochPri3\noreNil2\nornAna1\nornAna2\noryCun2\noryLat2\notoGar3\noviAri1\noviAri3\noviAri4\npanPan1\npanPan2\npanTro1\npanTro2\npanTro3\npanTro4\npanTro5\npanTro6\npapAnu2\npapHam1\npetMar1\npetMar2\nponAbe2\nponAbe3\npriPac1\nproCap1\npteVam1\nrheMac2\nrheMac3\nrheMac8\nrhiRox1\nrn4\nrn5\nrn6\nsacCer1\nsacCer2\nsacCer3\nsaiBol1\nsarHar1\nsorAra1\nsorAra2\nspeTri2\nstrPur1\nstrPur2\nsusScr11\nsusScr2\nsusScr3\ntaeGut1\ntaeGut2\ntarSyr1\ntarSyr2\ntetNig1\ntetNig2\nthaSir1\ntriMan1\ntupBel1\nturTru2\nventer1\nvicPac1\nvicPac2\nxenLae2\nxenTro1\nxenTro2\nxenTro3\nxenTro7\nxenTro9`.split(/\\r?\\n/)\n","import { HubFile, SingleFileHub } from '@gmod/ucsc-hub'\nimport {\n generateTracks,\n fetchGenomesFile,\n fetchTrackDbFile,\n} from './ucscTrackHub'\n\nimport { AnyConfigurationModel, getConf } from '@jbrowse/core/configuration'\nimport { FileLocation, getSession } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { nanoid } from '@jbrowse/core/util/nanoid'\n\nfunction resolve(uri: string, baseUri: string) {\n return new URL(uri, baseUri).href\n}\n\nexport async function doConnect(self: {\n configuration: AnyConfigurationModel\n addTrackConfs: (arg: Record<string, unknown>[]) => void\n}) {\n const session = getSession(self)\n const notLoadedAssemblies = [] as string[]\n try {\n const hubFileLocation = getConf(self, 'hubTxtLocation') as FileLocation\n const hubFileText = await openLocation(hubFileLocation).readFile('utf8')\n // @ts-expect-error\n const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri)\n const { assemblyManager } = session\n if (hubFileText.includes('useOneFile on')) {\n const hub = new SingleFileHub(hubFileText)\n const { genome, tracks } = hub\n const genomeName = genome.name!\n\n const asm = assemblyManager.get(genomeName)\n if (!asm) {\n // @ts-expect-error\n session.addSessionAssembly({\n name: genomeName,\n sequence: {\n type: 'ReferenceSequenceTrack',\n trackId: `${genomeName}-${nanoid()}`,\n adapter: {\n type: 'TwoBitAdapter',\n twoBitLocation: {\n uri: resolve(genome.data.twoBitPath!, hubUri),\n },\n chromSizesLocation: {\n uri: resolve(genome.data.chromSizes!, hubUri),\n },\n },\n },\n })\n }\n const asm2 = assemblyManager.get(genomeName)\n const sequenceAdapter = getConf(asm2!, ['sequence', 'adapter'])\n const tracksNew = generateTracks({\n trackDb: tracks,\n trackDbLoc: hubFileLocation,\n assemblyName: genomeName,\n sequenceAdapter,\n })\n self.addTrackConfs(tracksNew)\n } else {\n const hubFile = new HubFile(hubFileText)\n const genomeFile = hubFile.data.genomesFile\n if (!genomeFile) {\n throw new Error('genomesFile not found on hub')\n }\n\n // @ts-expect-error\n const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri)\n const genomesFileLocation = hubUri\n ? {\n uri: resolve(genomeFile, hubUri),\n locationType: 'UriLocation' as const,\n }\n : {\n localPath: genomeFile,\n locationType: 'LocalPathLocation' as const,\n }\n const genomesFile = await fetchGenomesFile(genomesFileLocation)\n const map = {} as Record<string, number>\n for (const [genomeName, genome] of Object.entries(genomesFile.data)) {\n const assemblyNames = getConf(self, 'assemblyNames')\n if (assemblyNames.length > 0 && !assemblyNames.includes(genomeName)) {\n continue\n }\n\n const asm = assemblyManager.get(genomeName)\n if (!asm) {\n notLoadedAssemblies.push(genomeName)\n continue\n }\n\n // @ts-expect-error\n const db = genome.data.trackDb\n if (!db) {\n throw new Error('genomesFile not found on hub')\n }\n const base = new URL(genomeFile, hubUri)\n const loc = hubUri\n ? {\n uri: new URL(db, base).href,\n locationType: 'UriLocation' as const,\n }\n : {\n localPath: db,\n locationType: 'LocalPathLocation' as const,\n }\n const trackDb = await fetchTrackDbFile(loc)\n const sequenceAdapter = getConf(asm, ['sequence', 'adapter'])\n const tracks = generateTracks({\n trackDb,\n trackDbLoc: loc,\n assemblyName: genomeName,\n sequenceAdapter,\n })\n self.addTrackConfs(tracks)\n map[genomeName] = tracks.length\n }\n\n const loadedAssemblies = Object.entries(map)\n const str1 = loadedAssemblies.length\n ? `Loaded data from these assemblies: ${loadedAssemblies\n .map(([key, val]) => `${key} (${val} tracks)`)\n .join(', ')}`\n : ''\n const str2 = notLoadedAssemblies.length\n ? `Skipped data from these assemblies: ${notLoadedAssemblies.join(\n ', ',\n )}`\n : ''\n session.notify([str1, str2].filter(f => !!f).join('. '), 'success')\n }\n } catch (e) {\n console.error(e)\n session.notifyError(`${getConf(self, 'name')}: \"${e}\"`, e)\n session.breakConnection?.(self.configuration)\n }\n}\n"],"names":["RaStanza","constructor","stanza","options","data","checkIndent","skipValidation","stanzaLines","currentIndent","continuedLine","trimEnd","split","line","Error","trim","startsWith","endsWith","trimmedLine","slice","trimStart","combinedLine","undefined","indent","match","sep","indexOf","this","nameKey","key","value","name","validate","RaFile","raFile","stanzas","map","every","raStanza","validateRequiredFieldsArePresent","requiredFields","description","missingFields","field","push","length","join","TrackDbFile","trackDbFile","super","trackName","track","Object","entries","trackKeys","keys","parentTrackKeys","Set","some","has","includes","settings","currentTrackName","parent","currentTrack","parentTracks","reverse","parentTrack","ret","GenomesFile","genomeName","genome","HubFile","SingleFileHub","hubText","hubSection","genomeSection","trackSections","hubData","validateHub","validateGenomeSection","tracks","async","fetchTrackDbFile","trackDbLoc","text","openLocation","readFile","makeLoc","first","base","uri","URL","baseUri","href","locationType","makeLocAlt","alt","makeLoc2","generateTracks","trackDb","assemblyName","sequenceAdapter","res","categories","trackType","type","shortLabel","bigDataUrl","bigDataIdx","bigDataIndex","isUri","isUriLocation","baseTrackType","toLowerCase","bigDataLocation","longLabel","category","adapter","bamLocation","index","location","cramLocation","craiLocation","bigBedLocation","bigWigLocation","vcfGzLocation","hicLocation","generateUnknownTrackConf","makeTrackConfig","p","filter","f","trackId","objectHash","assemblyNames","notEmpty","resolve","doConnect","self","session","getSession","notLoadedAssemblies","hubFileLocation","getConf","hubFileText","hubUri","assemblyManager","hub","get","addSessionAssembly","sequence","nanoid","twoBitLocation","twoBitPath","chromSizesLocation","chromSizes","asm2","tracksNew","addTrackConfs","genomeFile","genomesFile","genomesFileLocation","localPath","genomesLoc","genomesFileText","fetchGenomesFile","asm","db","loc","loadedAssemblies","str1","val","str2","notify","e","console","error","notifyError","breakConnection","configuration"],"sourceRoot":""}

Mercurial > repos > fubar > jbrowse2

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