@jbrowse/plugin-legacy-jbrowse 2.6.1 → 2.6.2

package/src/JBrowse1Connection/jb1ToJb2.ts

@@ -1,529 +0,0 @@
-import { openLocation } from '@jbrowse/core/util/io'
-import { objectHash } from '@jbrowse/core/util'
-import {
-  generateUnknownTrackConf,
-  generateUnsupportedTrackConf,
-  guessAdapter,
-  guessTrackType,
-  UNKNOWN,
-  UNSUPPORTED,
-} from '@jbrowse/core/util/tracks'
-import { Track, RefSeqs, RefSeq } from './types'
-
-interface Jb2Track {
-  trackId: string
-  name: string
-  description?: string
-  category?: string[]
-  adapter?: Jb2Adapter
-  type?: string
-  defaultRendering?: string
-}
-
-interface Jb2Adapter {
-  type: string
-  features?: Jb2Feature[]
-  bamLocation?: Jb2Location
-  cramLocation?: Jb2Location
-  craiLocation?: Jb2Location
-  fastaLocation?: Jb2Location
-  faiLocation?: Jb2Location
-  gziLocation?: Jb2Location
-  twoBitLocation?: Jb2Location
-  bigWigLocation?: Jb2Location
-  bigBedLocation?: Jb2Location
-  vcfGzLocation?: Jb2Location
-  gffLocation?: Jb2Location
-  gffGzLocation?: Jb2Location
-  gtfLocation?: Jb2Location
-  bedGzLocation?: Jb2Location
-  index?: { location: Jb2Location; indexType?: string }
-  rootUrlTemplate?: Jb2Location
-  sequenceAdapter?: Jb2Adapter
-}
-
-interface Jb2Feature {
-  refName: string
-  uniqueId: string
-  start: number
-  end: number
-}
-
-interface Jb2Location {
-  uri?: string
-  localPath?: string
-  blobId?: string
-  locationType?: string
-}
-
-export function convertTrackConfig(
-  jb1TrackConfig: Track,
-  dataRoot: string,
-  sequenceAdapter: Jb2Adapter,
-): Jb2Track {
-  const jb2TrackConfig: Jb2Track = {
-    trackId: objectHash(jb1TrackConfig),
-    name: jb1TrackConfig.key || jb1TrackConfig.label,
-  }
-
-  const description =
-    jb1TrackConfig.metadata &&
-    (jb1TrackConfig.metadata.description || jb1TrackConfig.metadata.Description)
-  if (description) {
-    jb2TrackConfig.description = description
-  }
-
-  const category =
-    jb1TrackConfig.category ||
-    (jb1TrackConfig.metadata && jb1TrackConfig.metadata.category)
-  jb2TrackConfig.category = category ? category.split(/\s*\/\s*/) : []
-
-  const { storeClass } = jb1TrackConfig
-  if (!jb1TrackConfig.urlTemplate) {
-    if (!(storeClass && storeClass.endsWith('FromConfig'))) {
-      const trackIdentifier = jb1TrackConfig.key || jb1TrackConfig.label
-      console.warn(
-        `Could not import JBrowse1 track "${trackIdentifier}" because it does not have a "urlTemplate" or is not a "FromConfig" track`,
-      )
-      return generateUnsupportedTrackConf(
-        jb2TrackConfig.name,
-        trackIdentifier,
-        jb2TrackConfig.category,
-      )
-    }
-    return generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig)
-  }
-
-  const resolveUrlTemplate = (urlTemplate: string) => {
-    return new URL(urlTemplate, `${dataRoot}/`).href
-      .replaceAll(/%7B/gi, '{')
-      .replaceAll(/%7D/gi, '}')
-  }
-  const urlTemplate = resolveUrlTemplate(jb1TrackConfig.urlTemplate)
-
-  if (storeClass) {
-    if (storeClass === 'JBrowse/Store/SeqFeature/BAM') {
-      const adapter: Jb2Adapter = {
-        type: 'BamAdapter',
-        bamLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-      }
-      if (jb1TrackConfig.baiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.baiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-        }
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-          indexType: 'CSI',
-        }
-      } else {
-        adapter.index = {
-          location: { uri: `${urlTemplate}.bai`, locationType: 'UriLocation' },
-        }
-      }
-      return {
-        ...jb2TrackConfig,
-        type: 'AlignmentsTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/CRAM') {
-      const adapter: Jb2Adapter = {
-        type: 'CramAdapter',
-        cramLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-        sequenceAdapter,
-      }
-      adapter.craiLocation = jb1TrackConfig.craiUrlTemplate
-        ? {
-            uri: resolveUrlTemplate(jb1TrackConfig.craiUrlTemplate),
-            locationType: 'UriLocation',
-          }
-        : {
-            uri: `${urlTemplate}.crai`,
-            locationType: 'UriLocation',
-          }
-      return {
-        ...jb2TrackConfig,
-        type: 'AlignmentsTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/NCList') {
-      return {
-        ...jb2TrackConfig,
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'NCListAdapter',
-          rootUrlTemplate: { uri: urlTemplate, locationType: 'UriLocation' },
-        },
-      }
-    }
-    if (
-      storeClass === 'JBrowse/Store/SeqFeature/BigWig' ||
-      storeClass === 'JBrowse/Store/BigWig'
-    ) {
-      if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
-        jb2TrackConfig.defaultRendering = 'xyplot'
-      } else if (
-        jb1TrackConfig.type &&
-        jb1TrackConfig.type.endsWith('Density')
-      ) {
-        jb2TrackConfig.defaultRendering = 'density'
-      }
-      return {
-        ...jb2TrackConfig,
-        type: 'QuantitativeTrack',
-        adapter: {
-          type: 'BigWigAdapter',
-          bigWigLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-        },
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTabix') {
-      const adapter: Jb2Adapter = {
-        type: 'VcfTabixAdapter',
-        vcfGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-      }
-      if (jb1TrackConfig.tbiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-        }
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-          indexType: 'CSI',
-        }
-      } else {
-        adapter.index = {
-          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-        }
-      }
-      return {
-        ...jb2TrackConfig,
-        type: 'VariantTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/VCFTribble') {
-      return generateUnsupportedTrackConf(
-        jb2TrackConfig.name,
-        `VCFTribble (${urlTemplate})`,
-        jb2TrackConfig.category,
-      )
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3') {
-      return {
-        ...jb2TrackConfig,
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'Gff3Adapter',
-          gffLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-        },
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/BigBed') {
-      return {
-        ...jb2TrackConfig,
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'BigBedAdapter',
-          bigBedLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-        },
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/GFF3Tabix') {
-      const adapter: Jb2Adapter = {
-        type: 'Gff3TabixAdapter',
-        gffGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-      }
-      if (jb1TrackConfig.tbiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-        }
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-          indexType: 'CSI',
-        }
-      } else {
-        adapter.index = {
-          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-        }
-      }
-      return {
-        ...jb2TrackConfig,
-        type: 'FeatureTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/BED') {
-      return generateUnsupportedTrackConf(
-        jb2TrackConfig.name,
-        `BED (${urlTemplate})`,
-        jb2TrackConfig.category,
-      )
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/BEDTabix') {
-      const adapter: Jb2Adapter = {
-        type: 'BedTabixAdapter',
-        bedGzLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-      }
-      if (jb1TrackConfig.tbiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.tbiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-        }
-      } else if (jb1TrackConfig.csiUrlTemplate) {
-        adapter.index = {
-          location: {
-            uri: resolveUrlTemplate(jb1TrackConfig.csiUrlTemplate),
-            locationType: 'UriLocation',
-          },
-          indexType: 'CSI',
-        }
-      } else {
-        adapter.index = {
-          location: { uri: `${urlTemplate}.tbi`, locationType: 'UriLocation' },
-        }
-      }
-      return {
-        ...jb2TrackConfig,
-        type: 'FeatureTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/GTF') {
-      return {
-        ...jb2TrackConfig,
-        type: 'FeatureTrack',
-        adapter: {
-          type: 'GtfAdapter',
-          gtfLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-        },
-      }
-    }
-    if (
-      storeClass === 'JBrowse/Store/SeqFeature/StaticChunked' ||
-      storeClass === 'JBrowse/Store/Sequence/StaticChunked'
-    ) {
-      return generateUnsupportedTrackConf(
-        jb2TrackConfig.name,
-        `StaticChunked (${urlTemplate})`,
-        jb2TrackConfig.category,
-      )
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/UnindexedFasta') {
-      return generateUnsupportedTrackConf(
-        jb2TrackConfig.name,
-        `UnindexedFasta (${urlTemplate})`,
-        jb2TrackConfig.category,
-      )
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta') {
-      const adapter: Jb2Adapter = {
-        type: 'IndexedFastaAdapter',
-        fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-      }
-      adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
-        ? {
-            uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-            locationType: 'UriLocation',
-          }
-        : {
-            uri: `${urlTemplate}.fai`,
-            locationType: 'UriLocation',
-          }
-      return {
-        ...jb2TrackConfig,
-        type: 'SequenceTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta') {
-      const adapter: Jb2Adapter = {
-        type: 'BgzipFastaAdapter',
-        fastaLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-      }
-      adapter.faiLocation = jb1TrackConfig.faiUrlTemplate
-        ? {
-            uri: resolveUrlTemplate(jb1TrackConfig.faiUrlTemplate),
-            locationType: 'UriLocation',
-          }
-        : {
-            uri: `${urlTemplate}.fai`,
-            locationType: 'UriLocation',
-          }
-      adapter.gziLocation = jb1TrackConfig.gziUrlTemplate
-        ? {
-            uri: resolveUrlTemplate(jb1TrackConfig.gziUrlTemplate),
-            locationType: 'UriLocation',
-          }
-        : {
-            uri: `${urlTemplate}.gzi`,
-            locationType: 'UriLocation',
-          }
-      return {
-        ...jb2TrackConfig,
-        type: 'ReferenceSequenceTrack',
-        adapter,
-      }
-    }
-    if (storeClass === 'JBrowse/Store/SeqFeature/TwoBit') {
-      return {
-        ...jb2TrackConfig,
-        type: 'ReferenceSequenceTrack',
-        adapter: {
-          type: 'TwoBitAdapter',
-          twoBitLocation: { uri: urlTemplate, locationType: 'UriLocation' },
-        },
-      }
-    }
-  }
-
-  // If we don't recognize the store class, make a best effort to guess by file type
-  jb2TrackConfig.adapter = guessAdapter(
-    { uri: urlTemplate, locationType: 'UriLocation' },
-    undefined,
-    urlTemplate,
-  )
-  if (!jb2TrackConfig.adapter) {
-    throw new Error('Could not determine adapter')
-  }
-
-  if (jb2TrackConfig.adapter.type === UNSUPPORTED) {
-    return generateUnsupportedTrackConf(
-      jb2TrackConfig.name,
-      urlTemplate,
-      jb2TrackConfig.category,
-    )
-  }
-  if (jb2TrackConfig.adapter.type === UNKNOWN) {
-    return generateUnknownTrackConf(
-      jb2TrackConfig.name,
-      urlTemplate,
-      jb2TrackConfig.category,
-    )
-  }
-
-  jb2TrackConfig.type = guessTrackType(jb2TrackConfig.adapter.type)
-
-  if (jb2TrackConfig.type === 'QuantitativeTrack') {
-    if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('XYPlot')) {
-      jb2TrackConfig.defaultRendering = 'xyplot'
-    } else if (jb1TrackConfig.type && jb1TrackConfig.type.endsWith('Density')) {
-      jb2TrackConfig.defaultRendering = 'density'
-    }
-  }
-
-  return jb2TrackConfig
-}
-
-function generateFromConfigTrackConfig(
-  jb1TrackConfig: Track,
-  jb2TrackConfig: Jb2Track,
-): Jb2Track {
-  const jb1Features = jb1TrackConfig.features || []
-  const jb2Features = jb1Features.map((feature): Jb2Feature => {
-    const jb2Feature: Jb2Feature = JSON.parse(JSON.stringify(feature))
-    jb2Feature.refName = feature.seq_id
-    jb2Feature.uniqueId = `${feature.seq_id}:${feature.start}-${feature.end}:${
-      feature.name || ''
-    }`
-    return jb2Feature
-  })
-  jb2TrackConfig.adapter = {
-    type: 'FromConfigAdapter',
-    features: jb2Features,
-  }
-  jb2TrackConfig.type = 'FeatureTrack'
-  return jb2TrackConfig
-}
-
-export async function createRefSeqsAdapter(
-  refSeqs: string | RefSeqs,
-): Promise<Jb2Adapter> {
-  if (typeof refSeqs === 'string') {
-    // assume refSeqs is a url if it is string
-    refSeqs = {
-      url: refSeqs,
-    }
-  }
-
-  // check refseq urls
-  if (refSeqs.url) {
-    if (refSeqs.url.match(/.fai$/)) {
-      return {
-        type: 'IndexedFastaAdapter',
-        fastaLocation: {
-          uri: refSeqs.url.slice(0, -4),
-          locationType: 'UriLocation',
-        },
-        faiLocation: {
-          uri: refSeqs.url,
-          locationType: 'UriLocation',
-        },
-      }
-    }
-    if (refSeqs.url.match(/.2bit$/)) {
-      return {
-        type: 'TwoBitAdapter',
-        twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
-      }
-    }
-    if (refSeqs.url.match(/.fa$/)) {
-      throw new Error('Unindexed FASTA adapter not available')
-    }
-    if (refSeqs.url.match(/.sizes/)) {
-      throw new Error('chromosome SIZES adapter not available')
-    }
-    const refSeqsJson = await openLocation({
-      uri: refSeqs.url,
-      locationType: 'UriLocation',
-    }).readFile('utf8')
-    const refSeqsData: RefSeq[] = JSON.parse(refSeqsJson)
-    return refSeqAdapterFromConfig(refSeqsData)
-  }
-  if ('data' in refSeqs) {
-    return refSeqAdapterFromConfig(refSeqs.data || [])
-  }
-  throw new Error(
-    `Could not determine adapter for JBrowse1 refSeqs: ${
-      refSeqs.url || JSON.stringify(refSeqs)
-    }`,
-  )
-}
-
-function refSeqAdapterFromConfig(refSeqsData: RefSeq[]): Jb2Adapter {
-  const features = refSeqsData.map(
-    (refSeq): Jb2Feature => ({
-      refName: refSeq.name,
-      uniqueId: refSeq.name,
-      start: refSeq.start,
-      end: refSeq.end,
-    }),
-  )
-  return {
-    type: 'FromConfigAdapter',
-    features,
-  }
-}

package/src/JBrowse1Connection/model.tsx

@@ -1,69 +0,0 @@
-import {
-  ConfigurationReference,
-  getConf,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { getSession } from '@jbrowse/core/util'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
-import { types } from 'mobx-state-tree'
-
-// locals
-import configSchema from './configSchema'
-
-export default function (pluginManager: PluginManager) {
-  return types
-    .compose(
-      'JBrowse1Connection',
-      BaseConnectionModelFactory(pluginManager),
-      types.model({
-        configuration: ConfigurationReference(configSchema),
-        type: types.literal('JBrowse1Connection'),
-      }),
-    )
-
-    .actions(self => ({
-      async connect() {
-        const session = getSession(self)
-        try {
-          const dataDirLocation = getConf(self, 'dataDirLocation')
-          const { fetchJb1 } = await import('./jb1ConfigLoad')
-          const { convertTrackConfig } = await import('./jb1ToJb2')
-          const config = await fetchJb1(dataDirLocation)
-          const assemblyName = getConf(self, 'assemblyNames')[0]
-          if (!assemblyName) {
-            throw new Error('assembly name required for JBrowse 1 connection')
-          }
-          const assemblyConf = session.assemblies.find(
-            a => readConfObject(a, 'name') === assemblyName,
-          )
-          if (!assemblyConf) {
-            throw new Error(`Assembly "${assemblyName}" not found`)
-          }
-          const sequenceAdapter = readConfObject(assemblyConf, [
-            'sequence',
-            'adapter',
-          ])
-
-          // @ts-expect-error
-          const jb2Tracks = config.tracks?.map(jb1Track => ({
-            ...convertTrackConfig(
-              jb1Track,
-              config.dataRoot || '',
-              sequenceAdapter,
-            ),
-            assemblyNames: [assemblyName],
-          }))
-
-          self.setTrackConfs(jb2Tracks)
-        } catch (error) {
-          console.error(error)
-          session.notify(
-            `There was a problem connecting to the JBrowse 1 data directory "${self.name}". Please make sure you have entered a valid location. The error that was thrown is: "${error}"`,
-            'error',
-          )
-          session.breakConnection(self.configuration)
-        }
-      },
-    }))
-}

package/src/JBrowse1Connection/types.ts

@@ -1,105 +0,0 @@
-export interface ProtoTrack {
-  backendVersion?: number
-  baseUrl?: string
-  category?: string
-  config?: Track
-  dataRoot?: string
-  features?: Feature[]
-  histograms?: Track
-  index?: number
-  key?: string
-  label?: string
-  metadata?: Metadata
-  store?: Store | string
-  storeClass?: string
-  type?: string
-  urlTemplate?: string
-  baiUrlTemplate?: string
-  craiUrlTemplate?: string
-  tbiUrlTemplate?: string
-  csiUrlTemplate?: string
-  faiUrlTemplate?: string
-  gziUrlTemplate?: string
-  useAsRefSeqStore?: boolean
-}
-
-export interface Track extends ProtoTrack {
-  label: string
-}
-
-export interface Metadata {
-  category?: string
-  description?: string
-  Description?: string
-}
-
-export interface Feature {
-  seq_id: string
-  start: number
-  end: number
-  name?: string
-}
-
-export interface Source {
-  url: string
-  name?: string
-  type?: string
-}
-
-export interface TrackMetadata {
-  sources?: string | Source | (string | Source)[] | Record<string, Source>
-}
-
-export interface Store extends ProtoTrack {
-  name?: string
-}
-
-export interface Names {
-  baseUrl?: string
-}
-
-export interface RefSeq {
-  name: string
-  length: number
-  end: number
-  start: number
-}
-
-export interface RefSeqs {
-  url?: string
-  data?: RefSeq[]
-}
-
-export interface Include {
-  url: string
-  cacheBuster?: boolean
-  format?: string
-  version?: number
-}
-
-export interface Config {
-  baseUrl?: string
-  cacheBuster?: boolean
-  dataRoot?: string
-  include?: string[]
-  names?: Record<string, string>
-  nameUrl?: string
-  refSeqs?: string | RefSeqs
-  sourceUrl?: string
-  stores?: Record<string, Store>
-  trackMetadata?: TrackMetadata
-  tracks?: Track | Track[] | Record<string, Track | ProtoTrack>
-}
-
-export interface UriLocation {
-  uri: string
-  baseUri?: string
-  locationType: 'UriLocation'
-}
-
-export interface LocalPathLocation {
-  localPath: string
-  locationType: 'LocalPathLocation'
-}
-
-export type JBLocation = UriLocation | LocalPathLocation