@jbrowse/plugin-data-management 2.3.1 → 2.3.2

package/src/ucsc-trackhub/ucscTrackHub.js

@@ -1,442 +0,0 @@
-import { objectHash } from '@jbrowse/core/util'
-import { openLocation } from '@jbrowse/core/util/io'
-import {
-  generateUnsupportedTrackConf,
-  generateUnknownTrackConf,
-} from '@jbrowse/core/util/tracks'
-import ucscAssemblies from './ucscAssemblies'
-
-export { ucscAssemblies }
-
-export async function fetchHubFile(hubFileLocation) {
-  try {
-    const hubFileText = await openLocation(hubFileLocation).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: '${error}'`)
-  }
-}
-
-export async function fetchGenomesFile(genomesFileLocation) {
-  const genomesFileText = await openLocation(genomesFileLocation).readFile(
-    'utf8',
-  )
-  const { GenomesFile } = await import('@gmod/ucsc-hub')
-  return new GenomesFile(genomesFileText)
-}
-
-export async function fetchTrackDbFile(trackDbFileLocation) {
-  const text = await openLocation(trackDbFileLocation).readFile('utf8')
-  const { TrackDbFile } = await import('@gmod/ucsc-hub')
-  return new TrackDbFile(text)
-}
-
-export function generateTracks(
-  trackDb,
-  trackDbFileLocation,
-  assemblyName,
-  sequenceAdapter,
-) {
-  const tracks = []
-
-  trackDb.forEach((track, trackName) => {
-    const trackKeys = Array.from(track.keys())
-    const parentTrackKeys = [
-      'superTrack',
-      'compositeTrack',
-      'container',
-      'view',
-    ]
-    if (trackKeys.some(key => parentTrackKeys.includes(key))) {
-      return
-    }
-    const parentTracks = []
-    let currentTrackName = trackName
-    do {
-      currentTrackName = trackDb.get(currentTrackName).get('parent')
-      if (currentTrackName) {
-        ;[currentTrackName] = currentTrackName.split(' ')
-        parentTracks.push(trackDb.get(currentTrackName))
-      }
-    } while (currentTrackName)
-    parentTracks.reverse()
-    const categories = parentTracks.map(parentTrack =>
-      parentTrack.get('shortLabel'),
-    )
-    const res = makeTrackConfig(
-      track,
-      categories,
-      trackDbFileLocation,
-      trackDb,
-      sequenceAdapter,
-    )
-    res.trackId = `ucsc-trackhub-${objectHash(res)}`
-    res.assemblyNames = [assemblyName]
-    tracks.push(res)
-  })
-
-  return tracks
-}
-
-function makeTrackConfig(
-  track,
-  categories,
-  trackDbFileLocation,
-  trackDb,
-  sequenceAdapter,
-) {
-  let trackType = track.get('type')
-  if (!trackType) {
-    trackType = trackDb.get(track.get('parent')).get('type')
-  }
-  let baseTrackType = trackType.split(' ')[0]
-  if (
-    baseTrackType === 'bam' &&
-    track.get('bigDataUrl').toLowerCase().endsWith('cram')
-  ) {
-    baseTrackType = 'cram'
-  }
-  let bigDataLocation
-  if (trackDbFileLocation.uri) {
-    bigDataLocation = {
-      uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
-      locationType: 'UriLocation',
-    }
-  } else {
-    bigDataLocation = {
-      localPath: track.get('bigDataUrl'),
-      locationType: 'LocalPathLocation',
-    }
-  }
-  let bigDataIndexLocation
-
-  switch (baseTrackType) {
-    case 'bam':
-      if (trackDbFileLocation.uri) {
-        bigDataIndexLocation = track.get('bigDataIndex')
-          ? {
-              uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
-                .href,
-              locationType: 'UriLocation',
-            }
-          : {
-              uri: new URL(
-                `${track.get('bigDataUrl')}.bai`,
-                trackDbFileLocation.uri,
-              ).href,
-              locationType: 'UriLocation',
-            }
-      } else {
-        bigDataIndexLocation = track.get('bigDataIndex')
-          ? {
-              localPath: track.get('bigDataIndex'),
-              locationType: 'LocalPathLocation',
-            }
-          : {
-              localPath: `${track.get('bigDataUrl')}.bai`,
-              locationType: 'LocalPathLocation',
-            }
-      }
-      return {
-        type: 'AlignmentsTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BamAdapter',
-          bamLocation: bigDataLocation,
-          index: {
-            location: bigDataIndexLocation,
-          },
-        },
-      }
-    case 'bed':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'bed5FloatScore':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'bedGraph':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'bedRnaElements':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'bigBarChart':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigBed':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'bigGenePred':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'bigChain':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigInteract':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigMaf':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigPsl':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-        renderer: {
-          type: 'SvgFeatureRenderer',
-        },
-      }
-    case 'bigWig':
-      return {
-        type: 'QuantitativeTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: bigDataLocation,
-        },
-      }
-    case 'broadPeak':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'coloredExon':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'cram':
-      if (trackDbFileLocation.uri) {
-        bigDataIndexLocation = track.get('bigDataIndex')
-          ? {
-              uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
-                .href,
-              locationType: 'UriLocation',
-            }
-          : {
-              uri: new URL(
-                `${track.get('bigDataUrl')}.crai`,
-                trackDbFileLocation.uri,
-              ).href,
-              locationType: 'UriLocation',
-            }
-      } else {
-        bigDataIndexLocation = track.get('bigDataIndex')
-          ? {
-              localPath: track.get('bigDataIndex'),
-              locationType: 'LocalPathLocation',
-            }
-          : {
-              localPath: `${track.get('bigDataUrl')}.crai`,
-              locationType: 'LocalPathLocation',
-            }
-      }
-      return {
-        type: 'AlignmentsTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'CramAdapter',
-          cramLocation: bigDataLocation,
-          craiLocation: bigDataIndexLocation,
-          sequenceAdapter,
-        },
-      }
-    case 'gvf':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'ld2':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'narrowPeak':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'bigNarrowPeak':
-      return {
-        type: 'FeatureTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: bigDataLocation,
-        },
-      }
-    case 'peptideMapping':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'vcfTabix':
-      if (trackDbFileLocation.uri) {
-        bigDataIndexLocation = track.get('bigDataIndex')
-          ? {
-              uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
-                .href,
-              locationType: 'UriLocation',
-            }
-          : {
-              uri: new URL(
-                `${track.get('bigDataUrl')}.tbi`,
-                trackDbFileLocation.uri,
-              ).href,
-              locationType: 'UriLocation',
-            }
-      } else {
-        bigDataIndexLocation = track.get('bigDataIndex')
-          ? {
-              localPath: track.get('bigDataIndex'),
-              locationType: 'LocalPathLocation',
-            }
-          : {
-              localPath: `${track.get('bigDataUrl')}.tbi`,
-              locationType: 'LocalPathLocation',
-            }
-      }
-      return {
-        type: 'VariantTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'VcfTabixAdapter',
-          vcfGzLocation: bigDataLocation,
-          index: {
-            location: bigDataIndexLocation,
-          },
-        },
-      }
-    case 'wig':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'wigMaf':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-    case 'hic':
-      return {
-        type: 'HicTrack',
-        name: track.get('shortLabel'),
-        description: track.get('longLabel'),
-        category: categories,
-        adapter: {
-          type: 'HicAdapter',
-          hicLocation: bigDataLocation,
-        },
-      }
-    case 'halSnake':
-      return generateUnsupportedTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-
-    default:
-      return generateUnknownTrackConf(
-        track.get('shortLabel'),
-        baseTrackType,
-        categories,
-      )
-  }
-}