@jbrowse/plugin-data-management 2.5.0 → 2.6.2

package/src/ucsc-trackhub/ucscTrackHub.ts

@@ -1,325 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import { RaStanza, TrackDbFile } from '@gmod/ucsc-hub'
-import { FileLocation, isUriLocation, objectHash } from '@jbrowse/core/util'
-import { openLocation } from '@jbrowse/core/util/io'
-import {
-  generateUnsupportedTrackConf,
-  generateUnknownTrackConf,
-} from '@jbrowse/core/util/tracks'
-
-export async function fetchHubFile(hubLocation: FileLocation) {
-  try {
-    const hubFileText = await openLocation(hubLocation).readFile('utf8')
-    const { HubFile } = await import('@gmod/ucsc-hub')
-    return new HubFile(hubFileText)
-  } catch (error) {
-    throw new Error(`Not a valid hub.txt file, got error: '${error}'`)
-  }
-}
-
-export async function fetchGenomesFile(genomesLoc: FileLocation) {
-  const genomesFileText = await openLocation(genomesLoc).readFile('utf8')
-  const { GenomesFile } = await import('@gmod/ucsc-hub')
-  return new GenomesFile(genomesFileText)
-}
-
-export async function fetchTrackDbFile(trackDbLoc: FileLocation) {
-  const text = await openLocation(trackDbLoc).readFile('utf8')
-  const { TrackDbFile } = await import('@gmod/ucsc-hub')
-  return new TrackDbFile(text)
-}
-
-export function makeLoc(first: string, base: { uri: string }) {
-  return {
-    uri: new URL(first, base.uri).href,
-    locationType: 'UriLocation',
-  }
-}
-
-export function makeLocAlt(first: string, alt: string, base: { uri: string }) {
-  return first ? makeLoc(first, base) : makeLoc(alt, base)
-}
-
-export function makeLoc2(first: string, alt?: string) {
-  return first
-    ? {
-        uri: first,
-        locationType: 'LocalPath',
-      }
-    : {
-        uri: alt,
-        locationType: 'UriLocation',
-      }
-}
-
-export function generateTracks(
-  trackDb: TrackDbFile,
-  trackDbLoc: FileLocation,
-  assemblyName: string,
-  sequenceAdapter: any,
-) {
-  const tracks: any = []
-
-  for (const [trackName, track] of trackDb.entries()) {
-    const trackKeys = [...track.keys()]
-    const parentTrackKeys = new Set([
-      'superTrack',
-      'compositeTrack',
-      'container',
-      'view',
-    ])
-    if (trackKeys.some(key => parentTrackKeys.has(key))) {
-      continue
-    }
-    const parentTracks = []
-    let currentTrackName = trackName
-    do {
-      currentTrackName = trackDb.get(currentTrackName)?.get('parent') || ''
-      if (currentTrackName) {
-        ;[currentTrackName] = currentTrackName.split(' ')
-        parentTracks.push(trackDb.get(currentTrackName))
-      }
-    } while (currentTrackName)
-    parentTracks.reverse()
-    const categories = parentTracks
-      .map(p => p?.get('shortLabel'))
-      .filter((f): f is string => !!f)
-    const res = makeTrackConfig(
-      track,
-      categories,
-      trackDbLoc,
-      trackDb,
-      sequenceAdapter,
-    )
-    tracks.push({
-      ...res,
-      trackId: `ucsc-trackhub-${objectHash(res)}`,
-      assemblyNames: [assemblyName],
-    })
-  }
-
-  return tracks
-}
-
-function makeTrackConfig(
-  track: RaStanza,
-  categories: string[],
-  trackDbLoc: FileLocation,
-  trackDb: TrackDbFile,
-  sequenceAdapter: any,
-) {
-  let trackType = track.get('type')
-  const name = track.get('shortLabel') || ''
-  const bigDataUrl = track.get('bigDataUrl') || ''
-  const bigDataIdx = track.get('bigDataIndex') || ''
-  const isUri = isUriLocation(trackDbLoc)
-  if (!trackType) {
-    trackType = trackDb.get(track.get('parent') || '')?.get('type')
-  }
-  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.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BamAdapter',
-          bamLocation: bigDataLocation,
-          index: {
-            location: isUri
-              ? makeLocAlt(bigDataIdx, bigDataUrl + '.bai', trackDbLoc)
-              : makeLoc2(bigDataIdx, bigDataUrl + '.bai'),
-          },
-        },
-      }
-
-    case 'bigBarChart':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigBed':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'bigGenePred':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'bigChain':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigInteract':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigMaf':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigPsl':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigWig':
-      return {
-        type: 'QuantitativeTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: bigDataLocation,
-        },
-      }
-
-    case 'cram':
-      return {
-        type: 'AlignmentsTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'CramAdapter',
-          cramLocation: bigDataLocation,
-          craiLocation: isUri
-            ? makeLocAlt(bigDataIdx, bigDataUrl + '.crai', trackDbLoc)
-            : makeLoc2(bigDataIdx, bigDataUrl + '.crai'),
-          sequenceAdapter,
-        },
-      }
-
-    case 'bigNarrowPeak':
-      return {
-        type: 'FeatureTrack',
-        name,
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'peptideMapping':
-      return generateUnsupportedTrackConf(name, baseTrackType, categories)
-    case 'vcfTabix':
-      return {
-        type: 'VariantTrack',
-        name,
-        description: track.get('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.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'HicAdapter',
-          hicLocation: bigDataLocation,
-        },
-      }
-
-    // unsupported types
-    //     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'