@jbrowse/plugin-legacy-jbrowse 2.6.1 → 2.6.2

package/src/JBrowse1Connection/util.ts

@@ -1,149 +0,0 @@
-import getValue from 'get-value'
-import { Track, Source } from './types'
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-export function isTrack(arg: any): arg is Track {
-  return arg && arg.label && typeof arg.label === 'string'
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-export function isSource(arg: any): arg is Source {
-  return arg && arg.url && typeof arg.url === 'string'
-}
-
-/**
- * updates a with values from b, recursively
- */
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-type Obj = Record<string, any>
-export function deepUpdate(a: Obj, b: Obj): Obj {
-  for (const prop of Object.keys(b)) {
-    if (
-      prop in a &&
-      typeof b[prop] === 'object' &&
-      typeof a[prop] === 'object'
-    ) {
-      deepUpdate(a[prop], b[prop])
-    } else if (a[prop] === undefined || b[prop] !== undefined) {
-      a[prop] = b[prop]
-    }
-  }
-  return a
-}
-
-/**
- * replace variables in a template string with values
- *
- * @param template - String with variable names in curly brackets
- * e.g., `http://foo/{bar}?arg={baz.foo}`
- * @param fillWith - object with attribute-value mappings
- * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`
- * @returns the template string with variables in fillWith replaced
- * e.g., 'htp://foo/someurl?arg=valueforbaz'
- */
-export function fillTemplate(template: string, fillWith: Obj): string {
-  return template.replaceAll(/{([\s\w.]+)}/g, (match, varName) => {
-    varName = varName.replaceAll(/\s+/g, '')
-    const fill = getValue(fillWith, varName)
-    if (fill !== undefined) {
-      return typeof fill === 'function' ? fill(varName) : fill
-    }
-    if (fillWith.callback) {
-      // @ts-expect-error
-      const v = fillWith.callback.call(this, varName)
-      if (v !== undefined) {
-        return v
-      }
-    }
-    return match
-  })
-}
-
-/**
- * Clones objects (including DOM nodes) and all children.
- * Warning: do not clone cyclic structures
- * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
- * @param src - The object to clone
- */
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-export function clone(src: any): any {
-  if (
-    !src ||
-    typeof src !== 'object' ||
-    Object.prototype.toString.call(src) === '[object Function]'
-  ) {
-    // null, undefined, any non-object, or function
-    return src // anything
-  }
-  if (src.nodeType && 'cloneNode' in src) {
-    // DOM Node
-    return src.cloneNode(true) // Node
-  }
-  if (src instanceof Date) {
-    // Date
-    return new Date(src.getTime()) // Date
-  }
-  if (src instanceof RegExp) {
-    // RegExp
-    return new RegExp(src) // RegExp
-  }
-  let r
-  let i
-  let l
-  if (Array.isArray(src)) {
-    // array
-    r = []
-    for (i = 0, l = src.length; i < l; ++i) {
-      if (i in src) {
-        r[i] = clone(src[i])
-      }
-    }
-    // we don't clone functions for performance reasons
-    //    }else if(d.isFunction(src)){
-    //      // function
-    //      r = function(){ return src.apply(this, arguments); };
-  } else {
-    // generic objects
-    r = src.constructor ? new src.constructor() : {}
-  }
-  return mixin(r, src, clone)
-}
-
-/**
- * Copies/adds all properties of source to dest; returns dest.
- * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
- *
- * All properties, including functions (sometimes termed "methods"), excluding
- * any non-standard extensions found in Object.prototype, are copied/added to
- * dest. Copying/adding each particular property is delegated to copyFunc
- * (if any); copyFunc defaults to the Javascript assignment operator if not
- * provided. Notice that by default, mixin executes a so-called "shallow copy"
- * and aggregate types are copied/added by reference.
- * @param dest - The object to which to copy/add all properties contained in
- * source.
- * @param source - The object from which to draw all properties to copy into dest.
- * @param copyFunc - The process used to copy/add a property in source; defaults
- * to the Javascript assignment operator.
- * @returns dest, as modified
- */
-function mixin(dest: Obj, source: Obj, copyFunc: Function): Obj {
-  let name
-  let s
-  const empty = {}
-  for (name in source) {
-    // the (!(name in empty) || empty[name] !== s) condition avoids copying
-    // properties in "source" inherited from Object.prototype.	 For example,
-    // if dest has a custom toString() method, don't overwrite it with the
-    // toString() method that source inherited from Object.prototype
-    s = source[name]
-    if (
-      !(name in dest) ||
-      // @ts-expect-error
-      (dest[name] !== s && (!(name in empty) || empty[name] !== s))
-    ) {
-      dest[name] = copyFunc ? copyFunc(s) : s
-    }
-  }
-
-  return dest // Object
-}

package/src/JBrowse1TextSearchAdapter/HttpMap.test.ts

@@ -1,49 +0,0 @@
-import path from 'path'
-import meta from '../../test_data/names/meta.json'
-import first from '../../test_data/names/0.json'
-import last from '../../test_data/names/f.json'
-import HttpMap from './HttpMap'
-
-test('read from meta', async () => {
-  const rootTemplate = path
-    .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-    .replaceAll('\\', '\\\\')
-
-  jest.spyOn(global, 'fetch').mockImplementation(url => {
-    const response = `${url}`.includes('names/meta.json') ? meta : {}
-    return Promise.resolve(new Response(JSON.stringify(response)))
-  })
-  const hashMap = new HttpMap({ url: rootTemplate })
-  await hashMap.getBucket('apple')
-
-  // test compress and hash hex characters are set after initial search
-  expect(await hashMap.getHashHexCharacters()).toBe(1)
-  expect(await hashMap.getCompress()).toBe(0)
-})
-test('get bucket contents', async () => {
-  const rootTemplate = path
-    .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-    .replaceAll('\\', '\\\\')
-
-  const spy = jest.spyOn(global, 'fetch')
-  spy.mockImplementation(url => {
-    let response = {}
-    if (`${url}`.includes('names/meta.json')) {
-      response = meta
-    }
-    if (`${url}`.includes('names/0.json')) {
-      response = first
-    }
-    if (`${url}`.includes('names/f.json')) {
-      response = last
-    }
-    return Promise.resolve(new Response(JSON.stringify(response)))
-  })
-  const hashMap = new HttpMap({ url: rootTemplate })
-
-  await hashMap.getBucket('apple')
-  expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/0.json`)
-
-  await hashMap.getBucket('apple3')
-  expect(spy).toHaveBeenLastCalledWith(`${rootTemplate}/f.json`)
-})

package/src/JBrowse1TextSearchAdapter/HttpMap.ts

@@ -1,100 +0,0 @@
-/**
- * Helper class allows reading names index generated in JBrowse1
- * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
- */
-import crc32 from 'buffer-crc32'
-
-export default class HttpMap {
-  url: string
-
-  constructor(args: { url: string }) {
-    // make sure url has a trailing slash
-    this.url = /\/$/.test(args.url) ? args.url : `${args.url}/`
-  }
-
-  /**
-   * loads meta.json file from names directory and reads number of hash_bits used
-   */
-  async readMeta() {
-    const meta = await this.loadFile('meta.json')
-    const { compress, track_names: tracks } = meta
-    const hashHexCharacters = Math.ceil(meta.hash_bits / 4)
-    return { hashHexCharacters, compress, tracks }
-  }
-
-  async getHashHexCharacters() {
-    const meta = await this.readMeta()
-    return meta.hashHexCharacters
-  }
-
-  async getCompress() {
-    const meta = await this.readMeta()
-    return meta.compress
-  }
-
-  async getTrackNames() {
-    const meta = await this.readMeta()
-    return meta.tracks
-  }
-
-  /**
-   * Returns contents of a bucket given a key
-   * @param key - string
-   */
-  async get(key: string) {
-    const bucket = await this.getBucket(key)
-    return bucket[key]
-  }
-
-  /**
-   * Returns a bucket given a key
-   * @param key - string
-   */
-  async getBucket(key: string) {
-    const bucketIdent = this.hash(key)
-    const hexToDirPath = await this.hexToDirPath(bucketIdent)
-    return this.loadFile(hexToDirPath)
-  }
-
-  /**
-   * Loads a file using the url and provided id.
-   * Returns response object with contents of the file
-   * @param id - string
-   */
-  async loadFile(id: string) {
-    const response = await fetch(`${this.url}${id}`)
-    if (!response.ok) {
-      throw new Error(`HTTP ${response.status} ${response.statusText}`)
-    }
-    return response.json()
-  }
-
-  /**
-   * Returns the corresponding path of the file given a hex string
-   * @param hex - hex string
-   */
-  async hexToDirPath(hex: string) {
-    // zero-pad the hex string to be 8 chars if necessary
-    const hashHexCharacters = await this.getHashHexCharacters()
-    if (hashHexCharacters) {
-      const compress = await this.getCompress()
-      while (hex.length < 8) {
-        hex = `0${hex}`
-      }
-      hex = hex.slice(8 - hashHexCharacters)
-      const dirpath = []
-      for (let i = 0; i < hex.length; i += 3) {
-        dirpath.push(hex.slice(i, i + 3))
-      }
-      return `${dirpath.join('/')}.json${compress ? 'z' : ''}`
-    }
-    return ''
-  }
-
-  hash(data: string) {
-    return crc32(Buffer.from(data))
-      .toString('hex')
-      .toLowerCase()
-      .replace('-', 'n')
-  }
-}

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts

@@ -1,101 +0,0 @@
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
-import path from 'path'
-import meta from '../../test_data/names/meta.json'
-import first from '../../test_data/names/0.json'
-import last from '../../test_data/names/f.json'
-import Adapter from './JBrowse1TextSearchAdapter'
-import configSchema from './configSchema'
-
-function mockFetch(url: RequestInfo | URL) {
-  let response = {}
-  if (`${url}`.includes('names/meta.json')) {
-    response = meta
-  }
-  if (`${url}`.includes('names/0.json')) {
-    response = first
-  }
-  if (`${url}`.includes('names/f.json')) {
-    response = last
-  }
-  return Promise.resolve(new Response(JSON.stringify(response)))
-}
-
-const rootTemplate = path
-  .join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
-  .replaceAll('\\', '\\\\')
-
-test('search upper case', async () => {
-  const spy = jest.spyOn(global, 'fetch')
-  spy.mockImplementation(mockFetch)
-
-  const adapter = new Adapter(
-    configSchema.create({
-      type: 'JBrowse1TextSearchAdapter',
-      textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
-      namesIndexLocation: {
-        uri: decodeURI(new URL(`file://${rootTemplate}`).href),
-        locationType: 'UriLocation',
-      },
-    }),
-  )
-  const results = await adapter.searchIndex({
-    searchType: 'prefix',
-    queryString: 'Apple',
-  })
-  // check results are of type BaseResult for prefix search
-  expect(results.length).toBeGreaterThan(0)
-  expect(results[0] instanceof BaseResult).toBeTruthy()
-  expect(results[0].getLabel()).toEqual('Apple1')
-  expect(results[1].getLabel()).toEqual('Apple2')
-  expect(results[2].getLabel()).toEqual('Apple3')
-
-  // exact search
-  const results2 = await adapter.searchIndex({
-    searchType: 'exact',
-    queryString: 'Apple3',
-  })
-  // check results are of type location for exact search
-  expect(results2.length).toEqual(5)
-  expect(results2.length).toBeGreaterThan(0)
-  expect(results2[0] instanceof BaseResult).toBeTruthy()
-  expect(results2[0].getLabel()).toEqual('Apple3')
-  expect(results2[0].getLocation()).toEqual('ctgA:17399-23000')
-})
-
-test('search lower case', async () => {
-  const spy = jest.spyOn(global, 'fetch')
-  spy.mockImplementation(mockFetch)
-
-  const adapter = new Adapter(
-    configSchema.create({
-      type: 'JBrowse1TextSearchAdapter',
-      textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
-      namesIndexLocation: {
-        uri: decodeURI(new URL(`file://${rootTemplate}`).href),
-        locationType: 'UriLocation',
-      },
-    }),
-  )
-  const results = await adapter.searchIndex({
-    searchType: 'prefix',
-    queryString: 'apple',
-  })
-  // check results are of type BaseResult for prefix search
-  expect(results.length).toBeGreaterThan(0)
-  expect(results[0] instanceof BaseResult).toBeTruthy()
-  expect(results[0].getLabel()).toEqual('Apple1')
-  expect(results[1].getLabel()).toEqual('Apple2')
-  expect(results[2].getLabel()).toEqual('Apple3')
-
-  // exact search
-  const results2 = await adapter.searchIndex({
-    searchType: 'exact',
-    queryString: 'apple3',
-  })
-  // check results are of type location for exact search
-  expect(results2.length).toEqual(5)
-  expect(results2.length).toBeGreaterThan(0)
-  expect(results2[0] instanceof BaseResult).toBeTruthy()
-  expect(results2[0].getLabel()).toEqual('Apple3')
-  expect(results2[0].getLocation()).toEqual('ctgA:17399-23000')
-})

package/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts

@@ -1,100 +0,0 @@
-import {
-  BaseTextSearchAdapter,
-  BaseTextSearchArgs,
-  BaseAdapter,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import HttpMap from './HttpMap'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-
-export interface TooManyHits {
-  name: string
-  hitLimit: number
-}
-
-interface SearchResults {
-  prefix: ({ name: string } | string)[]
-  exact: [string, number, string, string, number, number][]
-}
-
-export type NamesIndexRecord = string | Array<string | number>
-
-type IndexFile = Record<string, SearchResults>
-
-// Uses index built by generate-names.pl
-export default class JBrowse1TextSearchAdapter
-  extends BaseAdapter
-  implements BaseTextSearchAdapter
-{
-  httpMap: HttpMap
-
-  tracksNames?: string[]
-
-  constructor(
-    config: AnyConfigurationModel,
-    getSubAdapter?: getSubAdapterType,
-    pluginManager?: PluginManager,
-  ) {
-    super(config, getSubAdapter, pluginManager)
-    const namesIndex = readConfObject(config, 'namesIndexLocation')
-    const { baseUri, uri } = namesIndex
-    this.httpMap = new HttpMap({
-      url: baseUri ? new URL(uri, baseUri).href : uri,
-    })
-  }
-
-  /**
-   * Returns the contents of the file containing the query if it exists
-   * else it returns empty
-   * @param query - string query
-   */
-  async loadIndexFile(query: string): Promise<IndexFile> {
-    return this.httpMap.getBucket(query)
-  }
-
-  async searchIndex(args: BaseTextSearchArgs) {
-    const { searchType, queryString } = args
-    const tracks = this.tracksNames || (await this.httpMap.getTrackNames())
-    const str = queryString.toLowerCase()
-    const entries = await this.loadIndexFile(str)
-    return entries[str]
-      ? this.formatResults(entries[str], tracks, searchType)
-      : []
-  }
-  formatResults(results: SearchResults, tracks: string[], searchType?: string) {
-    return [
-      ...(searchType === 'exact'
-        ? []
-        : results.prefix.map(
-            result =>
-              new BaseResult({
-                label: typeof result === 'object' ? result.name : result,
-                matchedAttribute: 'name',
-                matchedObject: { result: result },
-              }),
-          )),
-      ...results.exact.map(result => {
-        const name = result[0]
-        const trackIndex = result[1]
-        const refName = result[3]
-        const start = result[4]
-        const end = result[5]
-        const locstring = `${refName || name}:${start}-${end}`
-        return new BaseResult({
-          locString: locstring,
-          label: name,
-          matchedAttribute: 'name',
-          matchedObject: result,
-          trackId: tracks[trackIndex],
-        })
-      }),
-    ].filter(result => result.getLabel() !== 'too many matches')
-  }
-
-  freeResources() {}
-}

package/src/JBrowse1TextSearchAdapter/configSchema.ts

@@ -1,44 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config JBrowse1TextSearchAdapter
- * note: metadata about tracks and assemblies covered by text search adapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-export default ConfigurationSchema(
-  'JBrowse1TextSearchAdapter',
-  {
-    /**
-     * #slot
-     */
-    namesIndexLocation: {
-      type: 'fileLocation',
-      defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
-      description: 'the location of the JBrowse1 names index data directory',
-    },
-    /**
-     * #slot
-     */
-    tracks: {
-      type: 'stringArray',
-      defaultValue: [],
-      description: 'List of tracks covered by text search adapter',
-    },
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-      description: 'List of assemblies covered by text search adapter',
-    },
-  },
-  {
-    explicitlyTyped: true,
-    /**
-     * #identifier
-     */
-    explicitIdentifier: 'textSearchAdapterId',
-  },
-)

package/src/JBrowse1TextSearchAdapter/index.ts

@@ -1,18 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType'
-
-// locals
-import AdapterClass from './JBrowse1TextSearchAdapter'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addTextSearchAdapterType(
-    () =>
-      new TextSearchAdapterType({
-        name: 'JBrowse1TextSearchAdapter',
-        configSchema,
-        AdapterClass,
-        description: 'A JBrowse 1 text search adapter',
-      }),
-  )
-}

package/src/NCListAdapter/NCListAdapter.test.ts

@@ -1,58 +0,0 @@
-import { toArray } from 'rxjs/operators'
-import path from 'path'
-import { LocalFile, GenericFilehandle } from 'generic-filehandle'
-import { firstValueFrom } from 'rxjs'
-import Adapter from './NCListAdapter'
-import configSchema from './configSchema'
-
-export function generateReadBuffer(
-  getFileFunction: (str: string) => GenericFilehandle,
-) {
-  return (request: Request) => {
-    const file = getFileFunction(request.url)
-    return file.readFile('utf8')
-  }
-}
-
-beforeEach(() => {
-  // @ts-expect-error
-  fetch.resetMocks()
-  // @ts-expect-error
-  fetch.mockResponse(
-    generateReadBuffer(
-      (url: string) =>
-        new LocalFile(path.join(__dirname, `../../test_data/${url}`)),
-    ),
-  )
-})
-
-test('adapter can fetch features from ensembl_genes test set', async () => {
-  const args = {
-    refNames: [],
-    rootUrlTemplate: {
-      uri: 'ensembl_genes/{refseq}/trackData.json',
-      locationType: 'UriLocation',
-    },
-  }
-  const adapter = new Adapter(configSchema.create(args))
-
-  const features = adapter.getFeatures({
-    assemblyName: 'volvox',
-    refName: '21',
-    start: 34960388,
-    end: 35960388,
-  })
-
-  const featArr = await firstValueFrom(features.pipe(toArray()))
-  expect(featArr[0].get('refName')).toBe('21')
-  expect(featArr[0].id()).toBe(`test-21,0,0,19,22,0`)
-  const featJson = featArr.map(f => f.toJSON())
-  expect(featJson.length).toEqual(94)
-  for (const feature of featJson) {
-    expect(feature).toMatchSnapshot({ uniqueId: expect.any(String) })
-  }
-
-  expect(await adapter.hasDataForRefName('ctgA')).toBe(false)
-  expect(await adapter.hasDataForRefName('21')).toBe(true)
-  expect(await adapter.hasDataForRefName('20')).toBe(false)
-})