@jbrowse/img 2.16.1 → 2.18.0

package/dist/index.js

@@ -5,11 +5,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const fs_1 = __importDefault(require("fs"));
 const yargs_1 = __importDefault(require("yargs"));
-// locals
 const parseArgv_1 = require("./parseArgv");
 const renderRegion_1 = require("./renderRegion");
-const util_1 = require("./util");
 const setupEnv_1 = __importDefault(require("./setupEnv"));
+const util_1 = require("./util");
 (0, setupEnv_1.default)();
 const err = console.error;
 console.error = (...p) => {
@@ -23,10 +22,6 @@ console.warn = (...p) => {
         warn(p);
     }
 };
-// note: yargs is actually unused except for printing help we do custom command
-// line parsing, see parseArgv.ts
-//
-// eslint-disable-next-line @typescript-eslint/no-floating-promises,@typescript-eslint/no-unused-expressions
 yargs_1.default
     .command('jb2export', 'Creates a jbrowse 2 image snapshot')
     .option('config', {
@@ -66,7 +61,6 @@ yargs_1.default
     type: 'number',
     default: 2048,
 })
-    // track types
     .option('configtracks', {
     description: 'A list of track labels from a config file',
     type: 'array',
@@ -103,7 +97,6 @@ yargs_1.default
     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',
@@ -144,9 +137,6 @@ const args = (0, parseArgv_1.standardizeArgv)((0, parseArgv_1.parseArgv)(process
         else {
             fs_1.default.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) {

package/dist/parseArgv.js

@@ -2,18 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseArgv = parseArgv;
 exports.standardizeArgv = standardizeArgv;
-// 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', []],
-// ])
 function parseArgv(argv) {
     const map = [];
     while (argv.length) {

package/dist/renderRegion.d.ts

@@ -1,4 +1,4 @@
-import { Entry } from './parseArgv';
+import type { Entry } from './parseArgv';
 export interface Opts {
     noRasterize?: boolean;
     loc?: string;

package/dist/renderRegion.js

@@ -5,11 +5,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.readData = readData;
 exports.renderRegion = renderRegion;
-const client_1 = require("react-dom/client");
-const react_linear_genome_view_1 = require("@jbrowse/react-linear-genome-view");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const path_1 = __importDefault(require("path"));
 const fs_1 = __importDefault(require("fs"));
+const path_1 = __importDefault(require("path"));
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const react_linear_genome_view_1 = require("@jbrowse/react-linear-genome-view");
+const client_1 = require("react-dom/client");
 const util_1 = require("./util");
 function read(file) {
     let res;
@@ -47,22 +47,15 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
     if (config) {
         addRelativePaths(configData, path_1.default.dirname(path_1.default.resolve(config)));
     }
-    // the session.json can be a raw session or a json file with a "session"
-    // attribute, which is what is exported via the "File->Export session" in
-    // jbrowse-web
     if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.session) {
         sessionData = sessionData.session;
     }
-    // only export first view
     if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.views) {
         sessionData.view = sessionData.views[0];
     }
-    // use assembly from file if a file existed
     if (assemblyData) {
         configData.assembly = assemblyData;
     }
-    // else check if it was an assembly name in a config file
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     else if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
         configData.assemblies.find(entry => entry.name === asm);
         if (asm) {
@@ -76,7 +69,6 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
             configData.assembly = configData.assemblies[0];
         }
     }
-    // else load fasta from command line
     else if (fasta) {
         const bgzip = fasta.endsWith('gz');
         configData.assembly = {
@@ -109,15 +101,12 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
             };
         }
     }
-    // throw if still no assembly
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!configData.assembly) {
         throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
     }
     if (tracksData) {
         configData.tracks = tracksData;
     }
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     else if (!configData.tracks) {
         configData.tracks = [];
     }
@@ -290,11 +279,8 @@ function readData({ assembly: asm, config, session, fasta, aliases, cytobands, d
         }
     });
     if (!defaultSession) {
-        // don't use defaultSession from config.json file, can result in assembly
-        // name confusion
         configData.defaultSession = undefined;
     }
-    // only allow an external manually specified session
     if (sessionData) {
         configData.defaultSession = sessionData;
     }
@@ -308,19 +294,16 @@ function process(trackEntry, view, extra = c => c) {
     const currentTrack = view.showTrack(extra(track));
     const display = currentTrack.displays[0];
     opts.forEach(opt => {
-        // apply height to any track
         if (opt.startsWith('height:')) {
             const [, height] = opt.split(':');
             if (height) {
                 display.setHeight(+height);
             }
         }
-        // apply sort to pileup
         else if (opt.startsWith('sort:')) {
             const [, type, tag] = opt.split(':');
             display.PileupDisplay.setSortedBy(type, tag);
         }
-        // apply color scheme to pileup
         else if (opt.startsWith('color:')) {
             const [, type, tag] = opt.split(':');
             if (display.PileupDisplay) {
@@ -330,19 +313,16 @@ function process(trackEntry, view, extra = c => c) {
                 display.setColor(type);
             }
         }
-        // force track to render even if maxbpperpx limit hit...
         else if (opt.startsWith('force:')) {
             const [, force] = opt.split(':');
             if (force) {
                 display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE });
             }
         }
-        // apply wiggle autoscale
         else if (opt.startsWith('autoscale:')) {
             const [, autoscale] = opt.split(':');
             display.setAutoscale(autoscale);
         }
-        // apply min and max score to wiggle
         else if (opt.startsWith('minmax:')) {
             const [, min, max] = opt.split(':');
             if (min) {
@@ -352,22 +332,18 @@ function process(trackEntry, view, extra = c => c) {
                 display.setMaxScore(+max);
             }
         }
-        // apply linear or log scale to wiggle
         else if (opt.startsWith('scaletype:')) {
             const [, scaletype] = opt.split(':');
             display.setScaleType(scaletype);
         }
-        // draw crosshatches on wiggle
         else if (opt.startsWith('crosshatch:')) {
             const [, val = 'false'] = opt.split(':');
             display.setCrossHatches((0, util_1.booleanize)(val));
         }
-        // turn off fill on bigwig with fill:false
         else if (opt.startsWith('fill:')) {
             const [, val = 'true'] = opt.split(':');
             display.setFill((0, util_1.booleanize)(val));
         }
-        // set resolution:superfine to use finer bigwig bin size
         else if (opt.startsWith('resolution:')) {
             let [, val = 1] = opt.split(':');
             if (val === 'fine') {

package/dist/setupEnv.js

@@ -24,43 +24,33 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = setupEnv;
-const node_fetch_1 = __importStar(require("node-fetch"));
-const jsdom_1 = require("jsdom");
+const util_1 = require("util");
 const canvas_1 = require("canvas");
+const jsdom_1 = require("jsdom");
+const node_fetch_1 = __importStar(require("node-fetch"));
 function setupEnv() {
-    // @ts-expect-error
+    addGlobalCanvasUtils();
+    addGlobalTextUtils();
+    addGlobalDocument();
+    addFetchPolyfill();
+}
+function addGlobalCanvasUtils() {
     global.nodeImage = canvas_1.Image;
-    // @ts-expect-error
     global.nodeCreateCanvas = canvas_1.createCanvas;
+}
+function addGlobalTextUtils() {
+    global.TextEncoder = util_1.TextEncoder;
+    global.TextDecoder = util_1.TextDecoder;
+}
+function addGlobalDocument() {
     const window = new jsdom_1.JSDOM('...').window;
     global.document = window.document;
-    // @ts-expect-error
     global.window = window;
-    // 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-expect-error
+    addFetchPolyfill();
+}
+function addFetchPolyfill() {
     global.fetch = node_fetch_1.default;
-    // @ts-expect-error
     global.Headers = node_fetch_1.Headers;
-    // @ts-expect-error
     global.Response = node_fetch_1.Response;
-    // @ts-expect-error
     global.Request = node_fetch_1.Request;
 }

package/dist/util.js

@@ -5,10 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.booleanize = booleanize;
 exports.convert = convert;
+const child_process_1 = require("child_process");
 const fs_1 = __importDefault(require("fs"));
 const tmp_1 = __importDefault(require("tmp"));
-const child_process_1 = require("child_process");
-// nice helper function from https://stackoverflow.com/questions/263965/
 function booleanize(str) {
     return str === 'false' ? false : !!str;
 }

package/esm/index.js

@@ -1,10 +1,9 @@
 import fs from 'fs';
 import yargs from 'yargs';
-// locals
-import { standardizeArgv, parseArgv } from './parseArgv';
+import { parseArgv, standardizeArgv } from './parseArgv';
 import { renderRegion } from './renderRegion';
-import { convert } from './util';
 import setupEnv from './setupEnv';
+import { convert } from './util';
 setupEnv();
 const err = console.error;
 console.error = (...p) => {
@@ -18,10 +17,6 @@ console.warn = (...p) => {
         warn(p);
     }
 };
-// note: yargs is actually unused except for printing help we do custom command
-// line parsing, see parseArgv.ts
-//
-// eslint-disable-next-line @typescript-eslint/no-floating-promises,@typescript-eslint/no-unused-expressions
 yargs
     .command('jb2export', 'Creates a jbrowse 2 image snapshot')
     .option('config', {
@@ -61,7 +56,6 @@ yargs
     type: 'number',
     default: 2048,
 })
-    // track types
     .option('configtracks', {
     description: 'A list of track labels from a config file',
     type: 'array',
@@ -98,7 +92,6 @@ yargs
     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',
@@ -139,9 +132,6 @@ const args = standardizeArgv(parseArgv(process.argv.slice(2)), [
         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) {

package/esm/parseArgv.js

@@ -1,15 +1,3 @@
-// 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) {
     const map = [];
     while (argv.length) {

package/esm/renderRegion.d.ts

@@ -1,4 +1,4 @@
-import { Entry } from './parseArgv';
+import type { Entry } from './parseArgv';
 export interface Opts {
     noRasterize?: boolean;
     loc?: string;

package/esm/renderRegion.js

@@ -1,8 +1,8 @@
-import { createRoot } from 'react-dom/client';
-import { createViewState } from '@jbrowse/react-linear-genome-view';
-import { renderToSvg, } from '@jbrowse/plugin-linear-genome-view';
-import path from 'path';
 import fs from 'fs';
+import path from 'path';
+import { renderToSvg } from '@jbrowse/plugin-linear-genome-view';
+import { createViewState } from '@jbrowse/react-linear-genome-view';
+import { createRoot } from 'react-dom/client';
 import { booleanize } from './util';
 function read(file) {
     let res;
@@ -40,22 +40,15 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
     if (config) {
         addRelativePaths(configData, path.dirname(path.resolve(config)));
     }
-    // the session.json can be a raw session or a json file with a "session"
-    // attribute, which is what is exported via the "File->Export session" in
-    // jbrowse-web
     if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.session) {
         sessionData = sessionData.session;
     }
-    // only export first view
     if (sessionData === null || sessionData === void 0 ? void 0 : sessionData.views) {
         sessionData.view = sessionData.views[0];
     }
-    // use assembly from file if a file existed
     if (assemblyData) {
         configData.assembly = assemblyData;
     }
-    // else check if it was an assembly name in a config file
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     else if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
         configData.assemblies.find(entry => entry.name === asm);
         if (asm) {
@@ -69,7 +62,6 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
             configData.assembly = configData.assemblies[0];
         }
     }
-    // else load fasta from command line
     else if (fasta) {
         const bgzip = fasta.endsWith('gz');
         configData.assembly = {
@@ -102,15 +94,12 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
             };
         }
     }
-    // throw if still no assembly
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (!configData.assembly) {
         throw new Error('no assembly specified, use --fasta to supply an indexed FASTA file (generated with samtools faidx yourfile.fa). see README for alternatives with --assembly and --config');
     }
     if (tracksData) {
         configData.tracks = tracksData;
     }
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     else if (!configData.tracks) {
         configData.tracks = [];
     }
@@ -283,11 +272,8 @@ export function readData({ assembly: asm, config, session, fasta, aliases, cytob
         }
     });
     if (!defaultSession) {
-        // don't use defaultSession from config.json file, can result in assembly
-        // name confusion
         configData.defaultSession = undefined;
     }
-    // only allow an external manually specified session
     if (sessionData) {
         configData.defaultSession = sessionData;
     }
@@ -301,19 +287,16 @@ function process(trackEntry, view, extra = c => c) {
     const currentTrack = view.showTrack(extra(track));
     const display = currentTrack.displays[0];
     opts.forEach(opt => {
-        // apply height to any track
         if (opt.startsWith('height:')) {
             const [, height] = opt.split(':');
             if (height) {
                 display.setHeight(+height);
             }
         }
-        // apply sort to pileup
         else if (opt.startsWith('sort:')) {
             const [, type, tag] = opt.split(':');
             display.PileupDisplay.setSortedBy(type, tag);
         }
-        // apply color scheme to pileup
         else if (opt.startsWith('color:')) {
             const [, type, tag] = opt.split(':');
             if (display.PileupDisplay) {
@@ -323,19 +306,16 @@ function process(trackEntry, view, extra = c => c) {
                 display.setColor(type);
             }
         }
-        // force track to render even if maxbpperpx limit hit...
         else if (opt.startsWith('force:')) {
             const [, force] = opt.split(':');
             if (force) {
                 display.setFeatureDensityStatsLimit({ bytes: Number.MAX_VALUE });
             }
         }
-        // apply wiggle autoscale
         else if (opt.startsWith('autoscale:')) {
             const [, autoscale] = opt.split(':');
             display.setAutoscale(autoscale);
         }
-        // apply min and max score to wiggle
         else if (opt.startsWith('minmax:')) {
             const [, min, max] = opt.split(':');
             if (min) {
@@ -345,22 +325,18 @@ function process(trackEntry, view, extra = c => c) {
                 display.setMaxScore(+max);
             }
         }
-        // apply linear or log scale to wiggle
         else if (opt.startsWith('scaletype:')) {
             const [, scaletype] = opt.split(':');
             display.setScaleType(scaletype);
         }
-        // draw crosshatches on wiggle
         else if (opt.startsWith('crosshatch:')) {
             const [, val = 'false'] = opt.split(':');
             display.setCrossHatches(booleanize(val));
         }
-        // turn off fill on bigwig with fill:false
         else if (opt.startsWith('fill:')) {
             const [, val = 'true'] = opt.split(':');
             display.setFill(booleanize(val));
         }
-        // set resolution:superfine to use finer bigwig bin size
         else if (opt.startsWith('resolution:')) {
             let [, val = 1] = opt.split(':');
             if (val === 'fine') {

package/esm/setupEnv.js

@@ -1,40 +1,30 @@
-import fetch, { Headers, Response, Request } from 'node-fetch';
-import { JSDOM } from 'jsdom';
+import { TextDecoder, TextEncoder } from 'util';
 import { Image, createCanvas } from 'canvas';
+import { JSDOM } from 'jsdom';
+import fetch, { Headers, Request, Response } from 'node-fetch';
 export default function setupEnv() {
-    // @ts-expect-error
+    addGlobalCanvasUtils();
+    addGlobalTextUtils();
+    addGlobalDocument();
+    addFetchPolyfill();
+}
+function addGlobalCanvasUtils() {
     global.nodeImage = Image;
-    // @ts-expect-error
     global.nodeCreateCanvas = createCanvas;
+}
+function addGlobalTextUtils() {
+    global.TextEncoder = TextEncoder;
+    global.TextDecoder = TextDecoder;
+}
+function addGlobalDocument() {
     const window = new JSDOM('...').window;
     global.document = window.document;
-    // @ts-expect-error
     global.window = window;
-    // 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-expect-error
+    addFetchPolyfill();
+}
+function addFetchPolyfill() {
     global.fetch = fetch;
-    // @ts-expect-error
     global.Headers = Headers;
-    // @ts-expect-error
     global.Response = Response;
-    // @ts-expect-error
     global.Request = Request;
 }

package/esm/util.js

@@ -1,7 +1,6 @@
+import { spawnSync } from 'child_process';
 import fs from 'fs';
 import tmp from 'tmp';
-import { spawnSync } from 'child_process';
-// nice helper function from https://stackoverflow.com/questions/263965/
 export function booleanize(str) {
     return str === 'false' ? false : !!str;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "main": "dist/index.js",
   "module": "esm/index.js",
   "author": "JBrowse Team",
@@ -27,8 +27,8 @@
     "@babel/runtime": "^7.17.9",
     "@emotion/cache": "^11.7.1",
     "@emotion/react": "^11.9.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.16.1",
-    "@jbrowse/react-linear-genome-view": "^2.16.1",
+    "@jbrowse/plugin-linear-genome-view": "^2.18.0",
+    "@jbrowse/react-linear-genome-view": "^2.18.0",
     "canvas": "^2.9.1",
     "jsdom": "^24.0.0",
     "mobx": "^6.6.0",
@@ -41,5 +41,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }