Format with lint

products/jbrowse-img/src/bin.js

@@ -1,2 +1,2 @@
 #!/usr/bin/env node
-require("./index.js");
+require('./index.js')

products/jbrowse-img/src/index.js

@@ -1,185 +1,187 @@
-import "abortcontroller-polyfill/dist/abortcontroller-polyfill-only";
-import fs from "fs";
-import yargs from "yargs";
-import { standardizeArgv, parseArgv } from "./parseArgv";
-import { renderRegion } from "./renderRegion";
-import tmp from "tmp";
+/* eslint-disable no-console */
+import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
+import fs from 'fs'
+import yargs from 'yargs'
+import { standardizeArgv, parseArgv } from './parseArgv'
+import { renderRegion } from './renderRegion'
+import tmp from 'tmp'
 
-import { spawnSync } from "child_process";
+import { spawnSync } from 'child_process'
 
+// eslint-disable-next-line no-unused-expressions
 yargs
-  .command("jb2export", "Creates a jbrowse 2 image snapshot")
-  .option("config", {
-    description: "Path to config file",
-    type: "string",
+  .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('session', {
+    description: 'Path to session file',
+    type: 'string',
   })
-  .option("assembly", {
+  .option('assembly', {
     description:
-      "Path to an assembly configuration, or a name of an assembly in the configFile",
-    type: "string",
+      '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('tracks', {
+    description: 'Path to tracks portion of a session',
+    type: 'string',
   })
-  .option("loc", {
+  .option('loc', {
     description:
-      "A locstring to navigate to, or --loc all to view the whole genome",
-    type: "string",
+      '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('fasta', {
+    description: 'Supply a fasta for the assembly',
+    type: 'string',
   })
-  .option("aliases", {
+  .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",
+      '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", {
+  .option('width', {
     description:
-      "Set the width of the window that jbrowse renders to, default: 1500px",
-    type: "number",
+      'Set the width of the window that jbrowse renders to, default: 1500px',
+    type: 'number',
   })
-  .option("pngwidth", {
+  .option('pngwidth', {
     description:
-      "Set the width of the png canvas if using png output, default 2048px",
-    type: "number",
+      '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('configtracks', {
+    description: 'A list of track labels from a config file',
+    type: 'array',
   })
-  .option("bam", {
+  .option('bam', {
     description:
-      "A bam file, flag --bam can be used multiple times to specify multiple bam files",
-    type: "array",
+      'A bam file, flag --bam can be used multiple times to specify multiple bam files',
+    type: 'array',
   })
-  .option("bigwig", {
+  .option('bigwig', {
     description:
-      "A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files",
-    type: "array",
+      'A bigwig file, the --bigwig flag can be used multiple times to specify multiple bigwig files',
+    type: 'array',
   })
-  .option("cram", {
+  .option('cram', {
     description:
-      "A cram file, the --cram flag can be used multiple times to specify multiple cram files",
-    type: "array",
+      'A cram file, the --cram flag can be used multiple times to specify multiple cram files',
+    type: 'array',
   })
-  .option("vcfgz", {
+  .option('vcfgz', {
     description:
-      "A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files",
-    type: "array",
+      'A tabixed VCF, the --vcfgz flag can be used multiple times to specify multiple vcfgz files',
+    type: 'array',
   })
-  .option("gffgz", {
+  .option('gffgz', {
     description:
-      "A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files",
-    type: "array",
+      'A tabixed GFF, the --gffgz can be used multiple times to specify multiple gffgz files',
+    type: 'array',
   })
-  .option("hic", {
+  .option('hic', {
     description:
-      "A .hic file, the --hic can be used multiple times to specify multiple hic files",
-    type: "array",
+      'A .hic file, the --hic can be used multiple times to specify multiple hic files',
+    type: 'array',
   })
-  .option("bigbed", {
+  .option('bigbed', {
     description:
-      "A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files",
-    type: "array",
+      'A .bigBed file, the --bigbed can be used multiple times to specify multiple bigbed files',
+    type: 'array',
   })
-  .option("bedgz", {
+  .option('bedgz', {
     description:
-      "A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files",
-    type: "array",
+      'A bed tabix file, the --bedgz can be used multiple times to specify multiple bedtabix files',
+    type: 'array',
   })
 
   // other
-  .option("out", {
+  .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",
+      '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", {
+  .option('noRasterize', {
     description:
-      "Use full SVG rendering with no rasterized layers, this can substantially increase filesize",
-    type: "boolean",
+      '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",
+  .option('defaultSession', {
+    description: 'Use the defaultSession from config.json',
+    type: 'boolean',
   })
   .help()
-  .alias("help", "h")
-  .alias("width", "w").argv;
+  .alias('help', 'h')
+  .alias('width', 'w').argv
 
-//prints to stderr the time it takes to execute cb
+// prints to stderr the time it takes to execute cb
 async function time(cb) {
-  const start = +Date.now();
-  const ret = await cb();
-  console.log(`Finished rendering: ${(+Date.now() - start) / 1000}s`);
-  return ret;
+  const start = +Date.now()
+  const ret = await cb()
+  console.log(`Finished rendering: ${(+Date.now() - start) / 1000}s`)
+  return ret
 }
 
 const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
-  "bam",
-  "cram",
-  "vcfgz",
-  "hic",
-  "bigwig",
-  "bigbed",
-  "bedgz",
-  "gffgz",
-  "configtracks",
-]);
+  'bam',
+  'cram',
+  'vcfgz',
+  'hic',
+  'bigwig',
+  'bigbed',
+  'bedgz',
+  'gffgz',
+  'configtracks',
+])
 
 time(() =>
-  renderRegion(args).then((result) => {
-    const outfile = args.out || "out.svg";
-    if (outfile.endsWith(".png")) {
+  renderRegion(args).then(result => {
+    const outfile = args.out || 'out.svg'
+    if (outfile.endsWith('.png')) {
       const tmpobj = tmp.fileSync({
         mode: 0o644,
-        prefix: "prefix-",
-        postfix: ".svg",
-      });
-      fs.writeFileSync(tmpobj.name, result);
-      const ls = spawnSync("rsvg-convert", [
-        "-w",
+        prefix: 'prefix-',
+        postfix: '.svg',
+      })
+      fs.writeFileSync(tmpobj.name, result)
+      const ls = spawnSync('rsvg-convert', [
+        '-w',
         args.pngwidth || 2048,
         tmpobj.name,
-        "-o",
+        '-o',
         outfile,
-      ]);
+      ])
 
-      console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`);
-      console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
-      fs.unlinkSync(tmpobj.name);
-    } else if (outfile.endsWith(".pdf")) {
+      console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`)
+      console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`)
+      fs.unlinkSync(tmpobj.name)
+    } else if (outfile.endsWith('.pdf')) {
       const tmpobj = tmp.fileSync({
         mode: 0o644,
-        prefix: "prefix-",
-        postfix: ".svg",
-      });
-      fs.writeFileSync(tmpobj.name, result);
-      const ls = spawnSync("rsvg-convert", [
-        "-w",
+        prefix: 'prefix-',
+        postfix: '.svg',
+      })
+      fs.writeFileSync(tmpobj.name, result)
+      const ls = spawnSync('rsvg-convert', [
+        '-w',
         args.pngwidth || 2048,
         tmpobj.name,
-        "-f",
-        "pdf",
-        "-o",
+        '-f',
+        'pdf',
+        '-o',
         outfile,
-      ]);
+      ])
 
-      console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`);
-      console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`);
-      fs.unlinkSync(tmpobj.name);
+      console.log(`rsvg-convert stderr: ${ls.stderr.toString()}`)
+      console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`)
+      fs.unlinkSync(tmpobj.name)
     } else {
-      fs.writeFileSync(outfile, result);
+      fs.writeFileSync(outfile, result)
     }
-  }, console.error)
-);
+  }, console.error),
+)

products/jbrowse-img/src/index.test.js

@@ -2,9 +2,11 @@ import { renderRegion } from './renderRegion'
 import fs from 'fs'
 
 function hashCode(str) {
-  var hash = 0
+  let hash = 0
   let chr
-  if (str.length === 0) return hash
+  if (str.length === 0) {
+    return hash
+  }
   for (let i = 0; i < str.length; i++) {
     chr = str.charCodeAt(i)
     hash = (hash << 5) - hash + chr
@@ -15,7 +17,7 @@ function hashCode(str) {
 
 const timeout = 20000
 
-//commented out for using remote files currently
+// commented out for using remote files currently
 xtest(
   'renders a region with --session and --config args',
   async () => {
@@ -29,7 +31,7 @@ xtest(
   timeout,
 )
 
-//commented out for using remote files currently
+// commented out for using remote files currently
 xtest(
   'renders a region with --session, --tracks, and --assembly args',
   async () => {
@@ -74,7 +76,7 @@ test(
   timeout,
 )
 
-//commented out for using remote files currently
+// commented out for using remote files currently
 xtest(
   'configtracks arg with urls',
   async () => {

products/jbrowse-img/src/parseArgv.js

@@ -1,29 +1,29 @@
 export function parseArgv(argv) {
-  const map = [];
+  const map = []
   while (argv.length) {
-    const val = argv[0].slice(2);
-    argv = argv.slice(1);
-    const next = argv.findIndex((arg) => arg.startsWith("-"));
+    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);
+      map.push([val, argv.slice(0, next)])
+      argv = argv.slice(next)
     } else {
-      map.push([val, argv]);
-      break;
+      map.push([val, argv])
+      break
     }
   }
-  return map;
+  return map
 }
 
 export function standardizeArgv(args, trackTypes) {
-  const result = { trackList: [] };
-  args.forEach((arg) => {
+  const result = { trackList: [] }
+  args.forEach(arg => {
     if (trackTypes.includes(arg[0])) {
-      result.trackList.push(arg);
+      result.trackList.push(arg)
     } else {
-      result[arg[0]] = arg[1][0] || true;
+      result[arg[0]] = arg[1][0] || true
     }
-  });
-  return result;
+  })
+  return result
 }