view x/static/js/5260.e7b7aeb6.chunk.js.map @ 125:49f3d3878413 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566

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false : seen.add(k)\n  })\n}\n\nexport default class Trix {\n  constructor(\n    public ixxFile: GenericFilehandle,\n    public ixFile: GenericFilehandle,\n    public maxResults = 20,\n  ) {}\n\n  async search(searchString: string, opts?: { signal?: AbortSignal }) {\n    let resultArr = [] as [string, string][]\n    const searchWords = searchString.split(' ')\n\n    // we only search one word at a time\n    const searchWord = searchWords[0].toLowerCase()\n    const res = await this._getBuffer(searchWord, opts)\n    if (!res) {\n      return []\n    }\n\n    let { end, buffer } = res\n    let done = false\n    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n    while (!done) {\n      let foundSomething = false\n      const str = buffer.toString()\n\n      // slice to lastIndexOf('\\n') to make sure we get complete records\n      // since the buffer fetch could get halfway into a record\n      const lines = str\n        .slice(0, str.lastIndexOf('\\n'))\n        .split('\\n')\n        .filter(f => !!f)\n\n      const hits2 = [] as string[]\n      for (const line of lines) {\n        const word = line.split(' ')[0]\n        const match = word.startsWith(searchWord)\n        if (!foundSomething && match) {\n          foundSomething = true\n        }\n\n        // we are done scanning if we are lexicographically greater than the\n        // search string\n        if (word.slice(0, searchWord.length) > searchWord) {\n          done = true\n        }\n        if (match) {\n          hits2.push(line)\n        }\n      }\n      const hits = hits2.flatMap(line => {\n        const [term, ...parts] = line.split(' ')\n        return parts.map(elt => [term, elt.split(',')[0]] as [string, string])\n      })\n\n      // if we are not done, and we haven't filled up maxResults with hits yet,\n      // then refetch\n      if (resultArr.length + hits.length < this.maxResults && !done) {\n        const res2 = await this.ixFile.read(\n          Buffer.alloc(CHUNK_SIZE),\n          0,\n          CHUNK_SIZE,\n          end,\n          opts,\n        )\n\n        // early break if empty response\n        if (!res2.bytesRead) {\n          resultArr = resultArr.concat(hits)\n          break\n        }\n        buffer = Buffer.concat([buffer, res2.buffer])\n        end += CHUNK_SIZE\n      }\n\n      // if we have filled up the hits, or we are detected to be done via the\n      // filtering, then return\n      else if (resultArr.length + hits.length >= this.maxResults || done) {\n        resultArr = resultArr.concat(hits)\n        break\n      }\n    }\n\n    // deduplicate results based on the detail column (resultArr[1])\n    return uniqBy(resultArr, elt => elt[1]).slice(0, this.maxResults)\n  }\n\n  private async getIndex(opts?: { signal?: AbortSignal }) {\n    const file = await this.ixxFile.readFile({\n      encoding: 'utf8',\n      ...opts,\n    })\n    return file\n      .split('\\n')\n      .filter(f => !!f)\n      .map(line => {\n        const p = line.length - ADDRESS_SIZE\n        const prefix = line.slice(0, p)\n        const posStr = line.slice(p)\n        const pos = Number.parseInt(posStr, 16)\n        return [prefix, pos] as const\n      })\n  }\n\n  private async _getBuffer(\n    searchWord: string,\n    opts?: { signal?: AbortSignal },\n  ) {\n    let start = 0\n    let end = 65536\n    const indexes = await this.getIndex(opts)\n    for (const [key, value] of indexes) {\n      const trimmedKey = key.slice(0, searchWord.length)\n      if (trimmedKey < searchWord) {\n        start = value\n        end = value + 65536\n      }\n    }\n\n    // Return the buffer and its end position in the file.\n    const len = end - start\n    if (len < 0) {\n      return undefined\n    }\n    const res = await this.ixFile.read(Buffer.alloc(len), 0, len, start, opts)\n    return {\n      ...res,\n      end,\n    }\n  }\n}\n","import Trix from '@gmod/trix'\nimport {\n  BaseTextSearchAdapter,\n  BaseAdapter,\n  BaseTextSearchArgs,\n} from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport BaseResult from '@jbrowse/core/TextSearch/BaseResults'\nimport {\n  AnyConfigurationModel,\n  readConfObject,\n} from '@jbrowse/core/configuration'\nimport PluginManager from '@jbrowse/core/PluginManager'\nimport { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\n\nfunction decodeURIComponentNoThrow(uri: string) {\n  try {\n    return decodeURIComponent(uri)\n  } catch (e) {\n    // avoid throwing exception on a failure to decode URI component\n    return uri\n  }\n}\n\nfunction shorten(str: string, term: string, w = 15) {\n  const tidx = str.toLowerCase().indexOf(term)\n\n  return str.length < 40\n    ? str\n    : (Math.max(0, tidx - w) > 0 ? '...' : '') +\n        str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() +\n        (tidx + term.length < str.length ? '...' : '')\n}\n\nexport default class TrixTextSearchAdapter\n  extends BaseAdapter\n  implements BaseTextSearchAdapter\n{\n  indexingAttributes?: string[]\n  trixJs: Trix\n  tracksNames?: string[]\n\n  constructor(\n    config: AnyConfigurationModel,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const ixFilePath = readConfObject(config, 'ixFilePath')\n    const ixxFilePath = readConfObject(config, 'ixxFilePath')\n\n    if (!ixFilePath) {\n      throw new Error('must provide out.ix')\n    }\n    if (!ixxFilePath) {\n      throw new Error('must provide out.ixx')\n    }\n    this.trixJs = new Trix(\n      openLocation(ixxFilePath, pluginManager),\n      openLocation(ixFilePath, pluginManager),\n      1500,\n    )\n  }\n\n  /**\n   * Returns list of results\n   * @param args - search options/arguments include: search query\n   * limit of results to return, searchType...prefix | full | exact\", etc.\n   */\n  async searchIndex(args: BaseTextSearchArgs) {\n    const query = args.queryString.toLowerCase()\n    const strs = query.split(' ')\n    const results = await this.trixJs.search(query)\n    const formatted = results\n      // if multi-word search try to filter out relevant items\n      .filter(([, data]) =>\n        strs.every(r =>\n          decodeURIComponentNoThrow(data).toLowerCase().includes(r),\n        ),\n      )\n      .map(([term, data]) => {\n        const result = JSON.parse(data.replaceAll('|', ',')) as string[]\n        const [loc, trackId, ...rest] = result.map(record =>\n          decodeURIComponentNoThrow(record),\n        )\n\n        const labelFieldIdx = rest.findIndex(elt => !!elt)\n        const contextIdx = rest\n          .map(elt => elt.toLowerCase())\n          .findIndex(f => f.includes(term.toLowerCase()))\n\n        const labelField = rest[labelFieldIdx]!\n        const contextField = rest[contextIdx]!\n        const context =\n          contextIdx !== -1 ? shorten(contextField, term) : undefined\n        const label = shorten(labelField, term)\n\n        const displayString =\n          !context || label.toLowerCase() === context.toLowerCase()\n            ? label\n            : `${label} (${context})`\n\n        return new BaseResult({\n          locString: loc,\n          label: labelField,\n          displayString,\n          matchedObject: result.map(record => decodeURIComponent(record)),\n          trackId,\n        })\n      })\n\n    return args.searchType === 'exact'\n      ? formatted.filter(\n          r => r.getLabel().toLowerCase() === args.queryString.toLowerCase(),\n        )\n      : formatted\n  }\n\n  freeResources() {}\n}\n"],"names":["CHUNK_SIZE","Trix","ixxFile","ixFile","maxResults","constructor","search","searchString","opts","resultArr","searchWord","split","toLowerCase","res","this","_getBuffer","end","buffer","done","foundSomething","str","toString","lines","slice","lastIndexOf","filter","f","hits2","line","word","match","startsWith","length","push","hits","flatMap","term","parts","map","elt","res2","read","alloc","bytesRead","concat","a","seen","Set","item","k","has","add","uniqBy","getIndex","readFile","encoding","p","prefix","posStr","Number","parseInt","start","indexes","key","value","len","decodeURIComponentNoThrow","uri","decodeURIComponent","e","shorten","w","tidx","indexOf","Math","max","trim","TrixTextSearchAdapter","BaseAdapter","config","getSubAdapter","pluginManager","super","ixFilePath","readConfObject","ixxFilePath","Error","trixJs","openLocation","searchIndex","args","query","queryString","strs","formatted","data","every","r","includes","result","JSON","parse","replaceAll","loc","trackId","rest","record","labelFieldIdx","findIndex","contextIdx","labelField","contextField","context","undefined","label","displayString","BaseResult","locString","matchedObject","searchType","getLabel","freeResources"],"sourceRoot":""}