myseq-vcf/lib/io/FileReaders-browser.js

Query local or remote Tabix-indexed VCFs by genomic position

"use strict";

function _defineProperty(obj, key, value) { if (key in obj) { Object.defineProperty(obj, key, { value: value, enumerable: true, configurable: true, writable: true }); } else { obj[key] = value; } return obj; }

/* global FileReader, fetch */
const AbstractFileReader = require('./AbstractFileReader');

class LocalFileReader extends AbstractFileReader {
  constructor(file) {
    super();

    _defineProperty(this, "file", void 0);

    _defineProperty(this, "size", void 0);

    this.file = file;
    this.size = file.size;
  }

  name() {
    return this.file.name;
  }

  bytes(start = 0, length) {
    return new Promise((resolve, reject) => {
      const lengthToRead = length === undefined ? this.size - start : length;
      const blob = this.file.slice(start, start + lengthToRead);
      const reader = new FileReader();

      reader.onload = () => {
        resolve(reader.result);
      };

      reader.onerror = () => {
        reject(reader.error);
      };

      reader.readAsArrayBuffer(blob);
    });
  }

}

class RemoteFileReader extends AbstractFileReader {
  constructor(url) {
    super();

    _defineProperty(this, "url", void 0);

    this.url = url;
  }

  bytes(start = 0, length) {
    const options = {
      method: 'GET'
    };

    if (start !== 0 || length !== undefined) {
      // Requesting only a portion of the file
      options.headers = {
        Range: length !== undefined ? `bytes=${start}-${start + (length - 1)}` : `bytes=${start}-`
      };
    } // https://github.com/webtorrent/webtorrent/issues/1193
    // Chrome will attempt to fulfill portions of a range request from the cache
    // occasionally resulting a failed fetch. Automatically retry fetch once on
    // an error while setting options to bypass the cache.


    return new Promise((resolve, reject) => {
      const wrappedFetch = (retry, addlOptions = {}) => {
        fetch(this.url, { ...options,
          ...addlOptions
        }).then(response => {
          if (response.ok) {
            resolve(response.arrayBuffer());
          } else {
            // Don't retry on HTTP error
            reject(new Error('Bad response from server'));
          }
        }).catch(error => {
          if (retry > 0) {
            wrappedFetch(retry - 1, { ...addlOptions,
              cache: 'reload'
            });
          } else {
            reject(error);
          }
        });
      };

      wrappedFetch(1);
    }); // return fetch(this.url, options).then((response) => {
    //   if (response.ok) {
    //     return response.arrayBuffer();
    //   }
    //   throw new Error('Bad response from server');
    // });
  }

}

module.exports = {
  LocalFileReader,
  RemoteFileReader
};