@jbrowse/plugin-legacy-jbrowse 2.6.1 → 2.6.3

package/esm/NCListAdapter/NCListFeature.js.map

@@ -1 +0,0 @@
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package/esm/NCListAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/esm/NCListAdapter/index.js.map

@@ -1 +0,0 @@
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package/esm/index.js.map

@@ -1 +0,0 @@
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package/src/GuessNCList/index.ts

@@ -1,27 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AdapterGuesser, getFileName } from '@jbrowse/core/util/tracks'
-import { FileLocation } from '@jbrowse/core/util/types'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /trackData.jsonz?$/i
-        const adapterName = 'NCListAdapter'
-        const fileName = getFileName(file)
-        if (regexGuess.test(fileName) || adapterHint === adapterName) {
-          return {
-            type: adapterName,
-            rootUrlTemplate: file,
-          }
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-}

package/src/JBrowse1Connection/configSchema.ts

@@ -1,42 +0,0 @@
-import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config JBrowse1Connection
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const JBrowse1Connection = ConfigurationSchema(
-  'JBrowse1Connection',
-  {
-    /**
-     * #slot
-     */
-    dataDirLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: 'http://mysite.com/jbrowse/data/',
-        locationType: 'UriLocation',
-      },
-      description:
-        'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
-    },
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      description:
-        'name of the assembly the connection belongs to, should be a single entry',
-      type: 'stringArray',
-      defaultValue: [],
-    },
-  },
-  {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: baseConnectionConfig,
-  },
-)
-
-export default JBrowse1Connection

package/src/JBrowse1Connection/index.ts

@@ -1,20 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'
-
-// locals
-import modelFactory from './model'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addConnectionType(
-    () =>
-      new ConnectionType({
-        name: 'JBrowse1Connection',
-        configSchema,
-        stateModel: modelFactory(pluginManager),
-        displayName: 'JBrowse 1 Data',
-        description: 'A JBrowse 1 data directory',
-        url: '//jbrowse.org/',
-      }),
-  )
-}

package/src/JBrowse1Connection/jb1ConfigLoad.ts

@@ -1,342 +0,0 @@
-import { openLocation } from '@jbrowse/core/util/io'
-import { parseJB1Json, parseJB1Conf, regularizeConf } from './jb1ConfigParse'
-import { clone, deepUpdate, fillTemplate } from './util'
-import {
-  JBLocation,
-  UriLocation,
-  LocalPathLocation,
-  Config,
-  Track,
-  Include,
-} from './types'
-
-function isUriLocation(location: JBLocation): location is UriLocation {
-  return (location as UriLocation).uri !== undefined
-}
-
-function isLocalPathLocation(
-  location: JBLocation,
-): location is LocalPathLocation {
-  return (location as LocalPathLocation).localPath !== undefined
-}
-
-export async function fetchJb1(
-  // eslint-disable-next-line unicorn/no-object-as-default-parameter
-  dataRoot: JBLocation = { uri: '', locationType: 'UriLocation' },
-  // eslint-disable-next-line unicorn/no-object-as-default-parameter
-  baseConfig: Config = {
-    include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],
-  },
-  // eslint-disable-next-line unicorn/no-object-as-default-parameter
-  baseConfigRoot: JBLocation = { uri: '', locationType: 'UriLocation' },
-): Promise<Config> {
-  const protocol = 'uri' in dataRoot ? 'uri' : 'localPath'
-  const dataRootReg = JSON.parse(JSON.stringify(dataRoot))
-  let dataRootLocation = ''
-  if (isUriLocation(dataRoot)) {
-    dataRootLocation = dataRoot.uri
-  }
-  if (isLocalPathLocation(dataRoot)) {
-    dataRootLocation = dataRoot.localPath
-  }
-  if (dataRootLocation.endsWith('/')) {
-    dataRootReg[protocol] = dataRootLocation.slice(0, -1)
-  }
-  if (
-    (isUriLocation(baseConfigRoot) && baseConfigRoot.uri) ||
-    (isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath)
-  ) {
-    const baseProtocol = 'uri' in baseConfigRoot ? 'uri' : 'localPath'
-    let baseConfigLocation = ''
-    if (isUriLocation(baseConfigRoot)) {
-      baseConfigLocation = baseConfigRoot.uri
-    }
-    if (isLocalPathLocation(baseConfigRoot)) {
-      baseConfigLocation = baseConfigRoot.localPath
-    }
-    if (baseConfigLocation.endsWith('/')) {
-      baseConfigLocation = baseConfigLocation.slice(0, -1)
-    }
-    let newConfig: Config = {}
-    for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {
-      let fetchedConfig = null
-      try {
-        // @ts-expect-error
-        fetchedConfig = await fetchConfigFile({
-          [baseProtocol]: `${baseConfigLocation}/${conf}`,
-        })
-      } catch (error) {
-        console.error(
-          `tried to access ${baseConfigLocation}/${conf}, but failed`,
-        )
-      }
-      newConfig = mergeConfigs(newConfig, fetchedConfig) || {}
-    }
-    if (dataRootReg[protocol]) {
-      newConfig.dataRoot = dataRootReg[protocol]
-    }
-    return createFinalConfig(newConfig)
-  }
-  const newConfig = regularizeConf(baseConfig, window.location.href)
-  if (dataRootReg[protocol]) {
-    newConfig.dataRoot = dataRootReg[protocol]
-  }
-  return createFinalConfig(newConfig)
-}
-
-export async function createFinalConfig(
-  baseConfig: Config,
-  defaults = configDefaults,
-): Promise<Config> {
-  const configWithDefaults = deepUpdate(clone(defaults), baseConfig)
-  let finalConfig = await loadIncludes(configWithDefaults)
-  finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig
-  fillTemplates(finalConfig, finalConfig)
-  validateConfig(finalConfig)
-  return finalConfig
-}
-
-export async function fetchConfigFile(location: JBLocation): Promise<Config> {
-  const result = await openLocation(location).readFile('utf8')
-  if (isUriLocation(location)) {
-    return parseJb1(result, location.uri)
-  }
-  if (isLocalPathLocation(location)) {
-    return parseJb1(result, location.localPath)
-  }
-  return parseJb1(result)
-}
-
-export function parseJb1(config: string, url = ''): Config {
-  if (config.trim().startsWith('{')) {
-    return parseJB1Json(config, url)
-  }
-  return parseJB1Conf(config, url)
-}
-
-/**
- * Merges config object b into a. Properties in b override those in a.
- */
-function mergeConfigs(a: Config | null, b: Config | null): Config | null {
-  if (b === null) {
-    return null
-  }
-
-  if (a === null) {
-    a = {}
-  }
-
-  for (const prop of Object.keys(b)) {
-    if (prop === 'tracks' && prop in a) {
-      const aTracks = a[prop] || []
-      const bTracks = b[prop] || []
-      if (Array.isArray(aTracks) && Array.isArray(bTracks)) {
-        a[prop] = mergeTrackConfigs(aTracks || [], bTracks || [])
-      } else {
-        throw new Error(
-          `Track config has not been properly regularized: ${aTracks} ${bTracks}`,
-        )
-      }
-    } else if (
-      !noRecursiveMerge(prop) &&
-      prop in a &&
-      // @ts-expect-error
-      typeof b[prop] === 'object' &&
-      // @ts-expect-error
-      typeof a[prop] === 'object'
-    ) {
-      // @ts-expect-error
-      a[prop] = deepUpdate(a[prop], b[prop])
-    } else if (prop === 'dataRoot') {
-      if (
-        a[prop] === undefined ||
-        (a[prop] === 'data' && b[prop] !== undefined)
-      ) {
-        a[prop] = b[prop]
-      }
-      // @ts-expect-error
-    } else if (a[prop] === undefined || b[prop] !== undefined) {
-      // @ts-expect-error
-      a[prop] = b[prop]
-    }
-  }
-  return a
-}
-
-/**
- * Special-case merging of two `tracks` configuration arrays.
- */
-function mergeTrackConfigs(a: Track[], b: Track[]): Track[] {
-  if (!b.length) {
-    return a
-  }
-
-  // index the tracks in `a` by track label
-  const aTracks: Record<string, Track> = {}
-  a.forEach((t, i): void => {
-    t.index = i
-    aTracks[t.label] = t
-  })
-
-  b.forEach((bT): void => {
-    const aT = aTracks[bT.label]
-    if (aT) {
-      mergeConfigs(aT, bT)
-    } else {
-      a.push(bT)
-    }
-  })
-
-  return a
-}
-
-/**
- * Recursively fetch, parse, and merge all the includes in the given config
- * object.  Calls the callback with the resulting configuration when finished.
- * @param inputConfig - Config to load includes into
- */
-async function loadIncludes(inputConfig: Config): Promise<Config> {
-  inputConfig = clone(inputConfig)
-
-  async function loadRecur(
-    config: Config,
-    upstreamConf: Config,
-  ): Promise<Config> {
-    const sourceUrl = config.sourceUrl || config.baseUrl
-    if (!sourceUrl) {
-      throw new Error(
-        `Could not determine source URL: ${JSON.stringify(config)}`,
-      )
-    }
-    const newUpstreamConf = mergeConfigs(clone(upstreamConf), config)
-    if (!newUpstreamConf) {
-      throw new Error('Problem merging configs')
-    }
-    const includes = fillTemplates(
-      regularizeIncludes(config.include || []),
-      newUpstreamConf,
-    )
-    delete config.include
-
-    const loads = includes.map(async (include): Promise<Config> => {
-      include.cacheBuster = inputConfig.cacheBuster
-      const includedData = await fetchConfigFile({
-        uri: new URL(include.url, sourceUrl).href,
-        locationType: 'UriLocation',
-      })
-      return loadRecur(includedData, newUpstreamConf)
-    })
-    const includedDataObjects = await Promise.all(loads)
-    includedDataObjects.forEach((includedData): void => {
-      config = mergeConfigs(config, includedData) || config
-    })
-    return config
-  }
-
-  return loadRecur(inputConfig, {})
-}
-
-function regularizeIncludes(
-  includes: Include | string | (Include | string)[] | null,
-): Include[] {
-  if (!includes) {
-    return []
-  }
-
-  // coerce include to an array
-  if (!Array.isArray(includes)) {
-    includes = [includes]
-  }
-
-  return includes.map((include): Include => {
-    // coerce bare strings in the includes to URLs
-    if (typeof include === 'string') {
-      include = { url: include }
-    }
-
-    // set defaults for format and version
-    if (!('format' in include)) {
-      include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json'
-    }
-    if (include.format === 'JB_json' && !('version' in include)) {
-      include.version = 1
-    }
-    return include
-  })
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any,@typescript-eslint/no-unnecessary-type-constraint
-function fillTemplates<T extends any>(subconfig: T, config: Config): T {
-  if (!subconfig) {
-    return subconfig
-  }
-  if (Array.isArray(subconfig)) {
-    for (let i = 0; i < subconfig.length; i += 1) {
-      subconfig[i] = fillTemplates(subconfig[i], config)
-    }
-  } else if (typeof subconfig === 'object') {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const sub = subconfig as Record<string, any>
-    for (const name of Object.keys(sub)) {
-      sub[name] = fillTemplates(sub[name], config)
-    }
-  } else if (typeof subconfig === 'string') {
-    // @ts-expect-error
-    return fillTemplate(subconfig, config)
-  }
-
-  return subconfig
-}
-
-/**
- * list of config properties that should not be recursively merged
- * @param propName - name of config property
- */
-function noRecursiveMerge(propName: string): boolean {
-  return propName === 'datasets'
-}
-
-const configDefaults = {
-  tracks: [],
-
-  containerID: 'GenomeBrowser',
-  dataRoot: 'data',
-  show_tracklist: true,
-  show_nav: true,
-  show_menu: true,
-  show_overview: true,
-  show_fullviewlink: true,
-  update_browser_title: true,
-  updateBrowserURL: true,
-
-  refSeqs: '{dataRoot}/seq/refSeqs.json',
-  include: ['jbrowse.conf', 'jbrowse_conf.json'],
-  nameUrl: '{dataRoot}/names/root.json',
-
-  datasets: {
-    _DEFAULT_EXAMPLES: true,
-    volvox: { url: '?data=sample_data/json/volvox', name: 'Volvox Example' },
-    modencode: {
-      url: '?data=sample_data/json/modencode',
-      name: 'MODEncode Example',
-    },
-    yeast: { url: '?data=sample_data/json/yeast', name: 'Yeast Example' },
-  },
-
-  highlightSearchedRegions: false,
-  highResolutionMode: 'auto',
-}
-
-/**
- * Examine the loaded and merged configuration for errors.  Throws
- * exceptions if it finds anything amiss.
- * @returns nothing meaningful
- */
-function validateConfig(config: Config): void {
-  if (!config.tracks) {
-    config.tracks = []
-  }
-  if (!config.baseUrl) {
-    throw new Error('Must provide a `baseUrl` in configuration')
-  }
-}