@jbrowse/img 2.1.7 → 2.2.1

package/src/index.ts

@@ -0,0 +1,209 @@
+import fs from 'fs'
+import yargs from 'yargs'
+import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
+import fetch, { Headers, Response, Request } from 'node-fetch'
+import { JSDOM } from 'jsdom'
+import { Image, createCanvas } from 'canvas'
+
+// locals
+import { standardizeArgv, parseArgv } from './parseArgv'
+import { renderRegion, Opts } from './renderRegion'
+import { convert } from './util'
+
+// @ts-ignore
+global.nodeImage = Image
+// @ts-ignore
+global.nodeCreateCanvas = createCanvas
+
+const { document } = new JSDOM(`...`).window
+global.document = document
+
+// force use of node-fetch polyfill, even if node 18+ fetch is available.
+// native node 18+ fetch currently gives errors related to unidici and
+// Uint8Array:
+//
+//
+// % node --version
+// v18.12.1
+//
+// % jb2export --fasta https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa --bam https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam --loc ctgA:1-1000 --out out4.svg
+// [
+//   '(node:1387934) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time\n' +
+//     '(Use `node --trace-warnings ...` to show where the warning was created)'
+// ]
+// [
+//   RangeError: offset is out of bounds
+//       at Uint8Array.set (<anonymous>)
+//       at Response.arrayBuffer (node:internal/deps/undici/undici:6117:23)
+//       at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
+// ]
+
+// @ts-ignore
+global.fetch = fetch
+// @ts-ignore
+global.Headers = Headers
+// @ts-ignore
+global.Response = Response
+// @ts-ignore
+global.Request = Request
+
+const err = console.error
+console.error = (...p: unknown[]) => {
+  if (!`${p[0]}`.match('useLayoutEffect')) {
+    err(p)
+  }
+}
+
+const warn = console.warn
+console.warn = (...p: unknown[]) => {
+  if (!`${p[0]}`.match('estimation reached timeout')) {
+    warn(p)
+  }
+}
+
+// note: yargs is actually unused except for printing help
+// we do custom command line parsing, see parseArgv.ts
+
+yargs
+  .command('jb2export', 'Creates a jbrowse 2 image snapshot')
+  .option('config', {
+    description: 'Path to config file',
+    type: 'string',
+  })
+  .option('session', {
+    description: 'Path to session file',
+    type: 'string',
+  })
+  .option('assembly', {
+    description:
+      'Path to an assembly configuration, or a name of an assembly in the configFile',
+    type: 'string',
+  })
+  .option('tracks', {
+    description: 'Path to tracks portion of a session',
+    type: 'string',
+  })
+  .option('loc', {
+    description:
+      'A locstring to navigate to, or --loc all to view the whole genome',
+    type: 'string',
+  })
+  .option('fasta', {
+    description: 'Supply a fasta for the assembly',
+    type: 'string',
+  })
+  .option('aliases', {
+    description:
+      'Supply aliases for the assembly, e.g. mapping of 1 to chr1. Tab separated file where column 1 matches the names from the FASTA',
+    type: 'string',
+  })
+  .option('width', {
+    description:
+      'Set the width of the window that jbrowse renders to, default: 1500px',
+    type: 'number',
+  })
+  .option('pngwidth', {
+    description:
+      'Set the width of the png canvas if using png output, default 2048px',
+    type: 'number',
+    default: 2048,
+  })
+  // track types
+  .option('configtracks', {
+    description: 'A list of track labels from a config file',
+    type: 'array',
+  })
+  .option('bam', {
+    description:
+      'A bam file, flag --bam can be used multiple times to specify multiple bam files',
+    type: 'array',
+  })
+  .option('bigwig', {
+    description:
+      'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
+    type: 'array',
+  })
+  .option('cram', {
+    description:
+      'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
+    type: 'array',
+  })
+  .option('vcfgz', {
+    description:
+      'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
+    type: 'array',
+  })
+  .option('gffgz', {
+    description:
+      'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
+    type: 'array',
+  })
+  .option('hic', {
+    description:
+      'A .hic file, the --hic can be used multiple times to specify multiple hic files',
+    type: 'array',
+  })
+  .option('bigbed', {
+    description:
+      'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
+    type: 'array',
+  })
+  .option('bedgz', {
+    description:
+      'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
+    type: 'array',
+  })
+
+  // other
+  .option('out', {
+    description:
+      'File to output to. Default: out.svg. If a filename with extension .png is supplied the program will try to automatically execute rsvg-convert to convert it to png',
+    type: 'string',
+    default: 'out.svg',
+  })
+  .option('noRasterize', {
+    description:
+      'Use full SVG rendering with no rasterized layers, this can substantially increase filesize',
+    type: 'boolean',
+  })
+  .option('defaultSession', {
+    description: 'Use the defaultSession from config.json',
+    type: 'boolean',
+  })
+  .help()
+  .alias('help', 'h')
+  .alias('width', 'w').argv
+
+const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
+  'bam',
+  'cram',
+  'vcfgz',
+  'hic',
+  'bigwig',
+  'bigbed',
+  'bedgz',
+  'gffgz',
+  'configtracks',
+])
+
+;(async () => {
+  try {
+    const result = await renderRegion(args as Opts)
+    const { out = 'out.svg', pngwidth = '2048' } = args
+    if (out.endsWith('.png')) {
+      convert(result, { out, pngwidth })
+    } else if (out.endsWith('.pdf')) {
+      convert(result, { out, pngwidth }, ['-f', 'pdf'])
+    } else {
+      fs.writeFileSync(out, result)
+    }
+
+    // manually exit the process after done rendering because autoruns or
+    // something similar otherwise keeps the nodejs process alive xref
+    // https://github.com/GMOD/jb2export/issues/6
+    process.exit(0)
+  } catch (e) {
+    console.error(e)
+    process.exit(1)
+  }
+})()

package/src/parseArgv.testmod.js

@@ -0,0 +1,29 @@
+import { parseArgv } from './parseArgv'
+
+test('parse', () => {
+  const args =
+    '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
+
+  expect(parseArgv(args.split(' '))).toEqual([
+    ['bam', ['dad.bam', 'color:red']],
+    ['vcf', ['variants.vcf']],
+    ['bam', ['mom.bam']],
+    ['defaultSession', []],
+    ['out', ['out.svg']],
+    ['noRasterize', []],
+  ])
+})
+
+test('parse', () => {
+  const args =
+    '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam force:true --defaultSession --out out.svg --noRasterize'
+
+  expect(parseArgv(args.split(' '))).toEqual([
+    ['bam', ['dad.bam', 'color:red']],
+    ['vcf', ['variants.vcf']],
+    ['bam', ['mom.bam', 'force:true']],
+    ['defaultSession', []],
+    ['out', ['out.svg']],
+    ['noRasterize', []],
+  ])
+})

package/src/parseArgv.ts

@@ -0,0 +1,48 @@
+export type Entry = [string, string[]]
+
+// example (see parseArgv.test.js):
+// const args =
+//   '--bam dad.bam color:red --vcf variants.vcf --bam mom.bam --defaultSession --out out.svg --noRasterize'
+//
+// expect(parseArgv(args.split(' '))).toEqual([
+//   ['bam', ['dad.bam', 'color:red']],
+//   ['vcf', ['variants.vcf']],
+//   ['bam', ['mom.bam']],
+//   ['defaultSession', []],
+//   ['out', ['out.svg']],
+//   ['noRasterize', []],
+// ])
+export function parseArgv(argv: string[]) {
+  const map = [] as Entry[]
+  while (argv.length) {
+    const val = argv[0].slice(2)
+    argv = argv.slice(1)
+    const next = argv.findIndex(arg => arg.startsWith('-'))
+
+    if (next !== -1) {
+      map.push([val, argv.slice(0, next)])
+      argv = argv.slice(next)
+    } else {
+      map.push([val, argv])
+      break
+    }
+  }
+  return map
+}
+
+export function standardizeArgv(args: Entry[], trackTypes: string[]) {
+  const result = { trackList: [] } as {
+    trackList: Entry[]
+    out?: string
+    pngwidth?: string
+    [key: string]: unknown
+  }
+  args.forEach(arg => {
+    if (trackTypes.includes(arg[0])) {
+      result.trackList.push(arg)
+    } else {
+      result[arg[0]] = arg[1][0] || true
+    }
+  })
+  return result
+}