@jbrowse/plugin-legacy-jbrowse 2.6.1 → 2.6.2

package/src/JBrowse1Connection/jb1ConfigParse.ts

@@ -1,423 +0,0 @@
-/* eslint no-cond-assign: ["error", "except-parens"] */
-import getValue from 'get-value'
-import setValue from 'set-value'
-import { objectHash } from '@jbrowse/core/util'
-import { isSource, isTrack } from './util'
-import { Config, Track, Source, Store, Names } from './types'
-
-export function parseJB1Json(config: Config | string, url: string): Config {
-  if (typeof config === 'string') {
-    let parsedConf
-    try {
-      parsedConf = JSON.parse(config)
-    } catch (error) {
-      throw new Error(`${error} when parsing configuration.`)
-    }
-    return regularizeConf(parsedConf, url)
-  }
-  return regularizeConf(config, url)
-}
-
-export function parseJB1Conf(config: string, url: string): Config {
-  let parsedConf
-  try {
-    parsedConf = parse(config, url)
-  } catch (error) {
-    throw new Error(`${error} when parsing configuration.`)
-  }
-  return regularizeConf(parsedConf, url)
-}
-
-function isAlwaysArray(varName: string): boolean {
-  if (varName === 'include') {
-    return true
-  }
-  return false
-}
-
-function parse(text: string, url: string): Config {
-  let section: string[] = []
-  let keyPath: string[] | undefined
-  let operation: string
-  let value: string | undefined
-  const data: Config = { tracks: {} }
-  let lineNumber: number
-
-  function recordVal(): void {
-    if (value !== undefined) {
-      let parsedValue:
-        | string
-        | number
-        | boolean
-        | string[]
-        | number[]
-        | boolean[]
-      try {
-        // parse json
-        const match = value.match(/^json:(.+)/i)
-        if (match) {
-          parsedValue = JSON.parse(match[1])
-        }
-        // parse numbers if it looks numeric
-        else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
-          parsedValue = parseFloat(value.replaceAll(',', ''))
-        } else {
-          parsedValue = value
-        }
-
-        if (!keyPath) {
-          throw new Error(`Error parsing in section ${section.join(' - ')}`)
-        }
-        const path = [...section, ...keyPath].join('.')
-        if (operation === '+=') {
-          let existing = getValue(data, path)
-          if (existing) {
-            if (!Array.isArray(existing)) {
-              existing = [existing]
-            }
-          } else {
-            existing = []
-          }
-
-          existing.push(parsedValue)
-          parsedValue = existing
-        }
-        if (parsedValue === 'true') {
-          parsedValue = true
-        }
-        if (parsedValue === 'false') {
-          parsedValue = false
-        }
-        setValue(data, path, parsedValue)
-      } catch (e) {
-        throw new Error(
-          `syntax error${url ? ` in ${url}` : ''}${
-            lineNumber ? ` at line ${lineNumber - 1}` : ''
-          }`,
-        )
-      }
-    }
-  }
-
-  text.split(/\n|\r\n|\r/).forEach((textLine, i): void => {
-    lineNumber = i + 1
-    const line = textLine.replace(/^\s*#.+/, '')
-
-    // new section
-    let match: RegExpMatchArray | null
-    if ((match = line.match(/^\s*\[([^\]]+)/))) {
-      // new section
-      recordVal()
-      keyPath = undefined
-      value = undefined
-      section = match[1].trim().split(/\s*\.\s*/)
-      if (section.length === 1 && section[0].toLowerCase() === 'general') {
-        section = []
-      }
-    }
-    // new value
-    else if (
-      (match = line.match(
-        value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/,
-      ))
-    ) {
-      recordVal()
-      keyPath = match[1].trim().split(/\s*\.\s*/)
-      ;[, , operation] = match
-      if (isAlwaysArray([...section, ...keyPath].join('.'))) {
-        operation = '+='
-      }
-      value = match[3].trim()
-    }
-    // add to existing array value
-    else if (
-      keyPath !== undefined &&
-      (match = line.match(/^\s{0,4}\+\s*(.+)/))
-    ) {
-      recordVal()
-      operation = '+='
-      value = match[1].trim()
-    }
-    // add to existing value
-    else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
-      value += value.length ? ` ${match[1].trim()}` : match[1].trim()
-    }
-    // done with last value
-    else {
-      recordVal()
-      keyPath = undefined
-      value = undefined
-    }
-  })
-
-  recordVal()
-
-  return data
-}
-
-/**
- * Applies defaults and any other necessary tweaks to the loaded configuration.
- * @param conf - the object containing the configuration, which it modifies
- * in-place
- * @param url - URL of the config file
- * @returns the same object it was passed
- */
-export function regularizeConf(conf: Config, url: string): Config {
-  // if tracks is not an array, convert it to one
-  if (conf.tracks && !Array.isArray(conf.tracks)) {
-    // if it's a single track config, wrap it in an arrayref
-    if (isTrack(conf.tracks)) {
-      conf.tracks = [conf.tracks]
-    }
-    // otherwise, coerce it to an array
-    else {
-      const tracks: Track[] = []
-      for (const label of Object.keys(conf.tracks)) {
-        const track = conf.tracks[label]
-        if (isTrack(track)) {
-          tracks.push(track)
-        } else {
-          tracks.push({ label, ...track })
-        }
-      }
-      conf.tracks = tracks
-    }
-  }
-
-  // regularize trackMetadata.sources
-  const meta = conf.trackMetadata
-  if (meta && meta.sources) {
-    // if it's a single source config, wrap it in an arrayref
-    if (typeof meta.sources === 'string') {
-      meta.sources = [meta.sources]
-    }
-    if (isSource(meta.sources)) {
-      meta.sources = [meta.sources]
-    }
-
-    if (!Array.isArray(meta.sources)) {
-      const sources: Source[] = []
-      for (const name of Object.keys(meta.sources)) {
-        const source = meta.sources[name]
-        if (!('name' in source)) {
-          source.name = name
-        }
-        sources.push(source)
-      }
-      meta.sources = sources
-    }
-
-    // coerce any string source defs to be URLs, and try to detect their types
-    meta.sources = meta.sources.map((sourceDef: string | Source): Source => {
-      if (typeof sourceDef === 'string') {
-        const newSourceDef: Source = { url: sourceDef }
-        const typeMatch = sourceDef.match(/\.(\w+)$/)
-        if (typeMatch) {
-          newSourceDef.type = typeMatch[1].toLowerCase()
-        }
-        return newSourceDef
-      }
-      return sourceDef
-    })
-  }
-
-  conf.sourceUrl = conf.sourceUrl || url
-  if (conf.sourceUrl.startsWith('/')) {
-    conf.sourceUrl = new URL(conf.sourceUrl, window.location.href).href
-  }
-  conf.baseUrl = conf.baseUrl || new URL('.', conf.sourceUrl).href
-  if (conf.baseUrl.length && !conf.baseUrl.endsWith('/')) {
-    conf.baseUrl += '/'
-  }
-
-  if (conf.sourceUrl) {
-    // set a default baseUrl in each of the track and store confs, and the names
-    // conf, if needed
-    const addBase: (Track | Store | Names)[] = []
-    if (conf.tracks) {
-      addBase.push(...conf.tracks)
-    }
-    if (conf.stores) {
-      addBase.push(...Object.values(conf.stores))
-    }
-    if (conf.names) {
-      addBase.push(conf.names)
-    }
-
-    addBase.forEach((t): void => {
-      if (!t.baseUrl) {
-        t.baseUrl = conf.baseUrl || '/'
-      }
-    })
-
-    // resolve the refSeqs and nameUrl if present
-    if (conf.refSeqs && typeof conf.refSeqs === 'string') {
-      conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href
-    }
-    if (conf.nameUrl) {
-      conf.nameUrl = new URL(conf.nameUrl, conf.sourceUrl).href
-    }
-  }
-
-  conf.stores = conf.stores || {}
-  ;(conf.tracks || []).forEach((trackConfig: Track): void => {
-    // if there is a `config` subpart, just copy its keys in to the top-level
-    // config
-    if (trackConfig.config) {
-      const c = trackConfig.config
-      delete trackConfig.config
-      trackConfig = { ...c, ...trackConfig }
-    }
-
-    // skip if it's a new-style track def
-    if (trackConfig.store) {
-      return
-    }
-
-    let trackClassName: string
-    if (trackConfig.type === 'FeatureTrack') {
-      trackClassName = 'JBrowse/View/Track/HTMLFeatures'
-    } else if (trackConfig.type === 'ImageTrack') {
-      trackClassName = 'JBrowse/View/Track/FixedImage'
-    } else if (trackConfig.type === 'ImageTrack.Wiggle') {
-      trackClassName = 'JBrowse/View/Track/FixedImage/Wiggle'
-    } else if (trackConfig.type === 'SequenceTrack') {
-      trackClassName = 'JBrowse/View/Track/Sequence'
-    } else {
-      trackClassName = regularizeClass('JBrowse/View/Track', trackConfig.type)
-    }
-
-    trackConfig.type = trackClassName
-
-    synthesizeTrackStoreConfig(conf, trackConfig)
-
-    if (trackConfig.histograms) {
-      if (!trackConfig.histograms.baseUrl) {
-        trackConfig.histograms.baseUrl = trackConfig.baseUrl
-      }
-      synthesizeTrackStoreConfig(conf, trackConfig.histograms)
-    }
-  })
-
-  return conf
-}
-
-/**
- * prefix class name with `root` if it contains no slashes
- * @param root - Prefix root
- * @param className - class name
- */
-function regularizeClass(root: string, className: string | undefined): string {
-  if (!className) {
-    return ''
-  }
-  if (!className.includes('/')) {
-    className = `${root}/${className}`
-  }
-  className = className.replace(/^\//, '')
-  return className
-}
-
-function guessStoreClass(
-  trackConfig: Track | undefined,
-  urlTemplate: string,
-): string {
-  if (!trackConfig) {
-    return ''
-  }
-  if (trackConfig.type && trackConfig.type.includes('/FixedImage')) {
-    return `JBrowse/Store/TiledImage/Fixed${
-      trackConfig.backendVersion === 0 ? '_v0' : ''
-    }`
-  }
-  if (/\.jsonz?$/i.test(urlTemplate)) {
-    return `JBrowse/Store/SeqFeature/NCList${
-      trackConfig.backendVersion === 0 ? '_v0' : ''
-    }`
-  }
-  if (/\.bam$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BAM'
-  }
-  if (/\.cram$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/CRAM'
-  }
-  if (/\.gff3?$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/GFF3'
-  }
-  if (/\.bed$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BED'
-  }
-  if (/\.vcf.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/VCFTabix'
-  }
-  if (/\.gff3?.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/GFF3Tabix'
-  }
-  if (/\.bed.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BEDTabix'
-  }
-  if (/\.(bw|bigwig)$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BigWig'
-  }
-  if (/\.(bb|bigbed)$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BigBed'
-  }
-  if (/\.(fa|fasta)$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/IndexedFasta'
-  }
-  if (/\.(fa|fasta)\.b?gz$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/BgzipIndexedFasta'
-  }
-  if (/\.2bit$/i.test(urlTemplate)) {
-    return 'JBrowse/Store/SeqFeature/TwoBit'
-  }
-  if (trackConfig.type && trackConfig.type.endsWith('/Sequence')) {
-    return 'JBrowse/Store/Sequence/StaticChunked'
-  }
-  return ''
-}
-
-function synthesizeTrackStoreConfig(
-  mainConf: Config,
-  trackConfig: Track,
-): void {
-  // figure out what data store class to use with the track, applying some
-  // defaults if it is not explicit in the configuration
-  const { urlTemplate = '' } = trackConfig
-
-  const storeClass = trackConfig.storeClass
-    ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
-    : guessStoreClass(trackConfig, urlTemplate)
-
-  if (!storeClass) {
-    console.warn(
-      `Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`,
-    )
-    return
-  }
-
-  // synthesize a separate store conf
-  const storeConf: Store = { ...trackConfig, type: storeClass }
-
-  // if this is the first sequence store we see, and we have no refseqs store
-  // defined explicitly, make this the refseqs store.
-  storeConf.name =
-    (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
-      storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
-      storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||
-      storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||
-      storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
-      storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
-      trackConfig.useAsRefSeqStore) &&
-    !(mainConf.stores && mainConf.stores.refseqs)
-      ? 'refseqs'
-      : `store${objectHash(storeConf)}`
-  // record it
-  if (!mainConf.stores) {
-    mainConf.stores = {}
-  }
-  mainConf.stores[storeConf.name] = storeConf
-
-  // connect it to the track conf
-  trackConfig.store = storeConf.name
-}