@jbrowse/img 2.2.0 → 2.2.2

package/esm/renderRegion.js

@@ -0,0 +1,366 @@
+import React from 'react';
+import { createViewState } from '@jbrowse/react-linear-genome-view';
+import { renderToSvg, } from '@jbrowse/plugin-linear-genome-view';
+import createCache from '@emotion/cache';
+import { CacheProvider } from '@emotion/react';
+import path from 'path';
+import fs from 'fs';
+import { booleanize } from './util';
+function read(file) {
+    let res;
+    try {
+        res = JSON.parse(fs.readFileSync(file, 'utf8'));
+    }
+    catch (e) {
+        throw new Error(`Failed to parse ${file} as JSON, use --fasta if you mean to pass a FASTA file`);
+    }
+    return res;
+}
+function makeLocation(file) {
+    return file.startsWith('http') ? { uri: file } : { localPath: file };
+}
+function addRelativePaths(config, configPath) {
+    if (typeof config === 'object') {
+        for (const key of Object.keys(config)) {
+            if (typeof config[key] === 'object') {
+                addRelativePaths(config[key], configPath);
+            }
+            else if (key === 'localPath') {
+                config.localPath = path.resolve(configPath, config.localPath);
+            }
+        }
+    }
+}
+export function readData({ assembly: asm, config, session, fasta, aliases, cytobands, defaultSession, tracks, trackList = [], }) {
+    var _a;
+    const assemblyData = asm && fs.existsSync(asm) ? read(asm) : undefined;
+    const tracksData = tracks ? read(tracks) : undefined;
+    const configData = (config ? read(config) : {});
+    let sessionData = session ? read(session) : undefined;
+    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
+    else if ((_a = configData.assemblies) === null || _a === void 0 ? void 0 : _a.length) {
+        configData.assemblies.find(entry => entry.name === asm);
+        if (asm) {
+            const assembly = configData.assemblies.find(entry => entry.name === asm);
+            if (!assembly) {
+                throw new Error(`assembly ${asm} not found in config`);
+            }
+            configData.assembly = assembly;
+        }
+        else {
+            configData.assembly = configData.assemblies[0];
+        }
+    }
+    // else load fasta from command line
+    else if (fasta) {
+        const bgzip = fasta.endsWith('gz');
+        configData.assembly = {
+            name: path.basename(fasta),
+            sequence: {
+                type: 'ReferenceSequenceTrack',
+                trackId: 'refseq',
+                adapter: {
+                    type: bgzip ? 'BgzipFastaAdapter' : 'IndexedFastaAdapter',
+                    fastaLocation: makeLocation(fasta),
+                    faiLocation: makeLocation(fasta + '.fai'),
+                    gziLocation: bgzip ? makeLocation(fasta + '.gzi') : undefined,
+                },
+            },
+        };
+        if (aliases) {
+            configData.assembly.refNameAliases = {
+                adapter: {
+                    type: 'RefNameAliasAdapter',
+                    location: makeLocation(aliases),
+                },
+            };
+        }
+        if (cytobands) {
+            configData.assembly.cytobands = {
+                adapter: {
+                    type: 'CytobandAdapter',
+                    location: makeLocation(cytobands),
+                },
+            };
+        }
+    }
+    // throw if still no assembly
+    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;
+    }
+    else if (!configData.tracks) {
+        configData.tracks = [];
+    }
+    trackList.forEach(track => {
+        const [type, [file]] = track;
+        if (type === 'bam') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'AlignmentsTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BamAdapter',
+                        bamLocation: makeLocation(file),
+                        index: { location: makeLocation(file + '.bai') },
+                        sequenceAdapter: configData.assembly.sequence.adapter,
+                    },
+                },
+            ];
+        }
+        if (type === 'cram') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'AlignmentsTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'CramAdapter',
+                        cramLocation: makeLocation(file),
+                        craiLocation: makeLocation(file + '.crai'),
+                        sequenceAdapter: configData.assembly.sequence.adapter,
+                    },
+                },
+            ];
+        }
+        if (type === 'bigwig') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'QuantitativeTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BigWigAdapter',
+                        bigWigLocation: makeLocation(file),
+                    },
+                },
+            ];
+        }
+        if (type === 'vcfgz') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'VariantTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'VcfTabixAdapter',
+                        vcfGzLocation: makeLocation(file),
+                        index: {
+                            location: makeLocation(file + '.tbi'),
+                        },
+                    },
+                },
+            ];
+        }
+        if (type === 'gffgz') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'FeatureTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'Gff3TabixAdapter',
+                        gffGzLocation: makeLocation(file),
+                        index: {
+                            location: makeLocation(file + '.tbi'),
+                        },
+                    },
+                },
+            ];
+        }
+        if (type === 'hic') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'HicTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'HicAdapter',
+                        hicLocation: makeLocation(file),
+                    },
+                },
+            ];
+        }
+        if (type === 'bigbed') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'FeatureTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BigBedAdapter',
+                        bigBedLocation: makeLocation(file),
+                    },
+                },
+            ];
+        }
+        if (type === 'bedgz') {
+            configData.tracks = [
+                ...configData.tracks,
+                {
+                    type: 'FeatureTrack',
+                    trackId: path.basename(file),
+                    name: path.basename(file),
+                    assemblyNames: [configData.assembly.name],
+                    adapter: {
+                        type: 'BedTabixAdapter',
+                        bedGzLocation: makeLocation(file),
+                        index: {
+                            location: makeLocation(file + '.tbi'),
+                        },
+                    },
+                },
+            ];
+        }
+    });
+    if (!defaultSession) {
+        // don't use defaultSession from config.json file, can result in assembly
+        // name confusion
+        delete configData.defaultSession;
+    }
+    // only allow an external manually specified session
+    if (sessionData) {
+        configData.defaultSession = sessionData;
+    }
+    return configData;
+}
+// without this, the styles can become messed up especially in lgv header
+// xref https://github.com/garronej/tss-react/issues/25
+export const muiCache = createCache({
+    key: 'mui',
+    prepend: true,
+});
+function process(trackEntry, view, extra = c => c) {
+    const [, [track, ...opts]] = trackEntry;
+    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(':');
+            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) {
+                display.PileupDisplay.setColorScheme({ type, tag });
+            }
+            else {
+                display.setColor(type);
+            }
+        }
+        // force track to render even if maxbpperpx limit hit...
+        else if (opt.startsWith('force:')) {
+            const [, force] = opt.split(':');
+            if (force) {
+                display.updateStatsLimit({ 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(':');
+            display.setMinScore(+min);
+            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] = opt.split(':');
+            display.setCrossHatches(booleanize(val));
+        }
+        // turn off fill on bigwig with fill:false
+        else if (opt.startsWith('fill:')) {
+            const [, val] = opt.split(':');
+            display.setFill(booleanize(val));
+        }
+        // set resolution:superfine to use finer bigwig bin size
+        else if (opt.startsWith('resolution:')) {
+            let [, val] = opt.split(':');
+            if (val === 'fine') {
+                val = '10';
+            }
+            else if (val === 'superfine') {
+                val = '100';
+            }
+            display.setResolution(+val);
+        }
+    });
+}
+export async function renderRegion(opts) {
+    const model = createViewState(readData(opts));
+    const { loc, width = 1500, trackList = [], session: sessionParam, defaultSession, } = opts;
+    const { session } = model;
+    const { view } = session;
+    const { assemblyManager } = model;
+    view.setWidth(width);
+    if (loc) {
+        const [assembly] = assemblyManager.assemblies;
+        if (loc === 'all') {
+            view.showAllRegionsInAssembly(assembly.name);
+        }
+        else {
+            await view.navToLocString(loc, assembly.name);
+        }
+    }
+    else if (!sessionParam && !defaultSession) {
+        console.warn('No loc specified');
+    }
+    trackList.forEach(track => {
+        process(track, view, extra => path.basename(extra));
+    });
+    return renderToSvg(view, {
+        rasterizeLayers: !opts.noRasterize,
+        ...opts,
+        Wrapper: ({ children }) => (React.createElement(CacheProvider, { value: muiCache }, children)),
+    });
+}
+//# sourceMappingURL=renderRegion.js.map

package/esm/renderRegion.js.map

@@ -0,0 +1 @@
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package/esm/util.d.ts

@@ -0,0 +1,5 @@
+export declare function booleanize(str: string): boolean;
+export declare function convert(result: string, args: {
+    out: string;
+    pngwidth?: string;
+}, spawnArgs?: string[]): void;

package/esm/util.js

@@ -0,0 +1,25 @@
+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;
+}
+function createTmp() {
+    return tmp.fileSync({
+        mode: 0o644,
+        prefix: 'prefix-',
+        postfix: '.svg',
+    });
+}
+export function convert(result, args, spawnArgs = []) {
+    const { name } = createTmp();
+    const { pngwidth = '2048', out } = args;
+    fs.writeFileSync(name, result);
+    const a = ['-w', pngwidth, name, '-o', out, ...spawnArgs];
+    const ls = spawnSync('rsvg-convert', a);
+    console.error(`rsvg-convert stderr: ${ls.stderr.toString()}`);
+    console.log(`rsvg-convert stdout: ${ls.stdout.toString()}`); // eslint-disable-line no-console
+    fs.unlinkSync(name);
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAA;AACnB,OAAO,GAAG,MAAM,KAAK,CAAA;AACrB,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AAEzC,wEAAwE;AACxE,MAAM,UAAU,UAAU,CAAC,GAAW;IACpC,OAAO,GAAG,KAAK,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;AACxC,CAAC;AAED,SAAS,SAAS;IAChB,OAAO,GAAG,CAAC,QAAQ,CAAC;QAClB,IAAI,EAAE,KAAK;QACX,MAAM,EAAE,SAAS;QACjB,OAAO,EAAE,MAAM;KAChB,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,OAAO,CACrB,MAAc,EACd,IAAwC,EACxC,YAAsB,EAAE;IAExB,MAAM,EAAE,IAAI,EAAE,GAAG,SAAS,EAAE,CAAA;IAC5B,MAAM,EAAE,QAAQ,GAAG,MAAM,EAAE,GAAG,EAAE,GAAG,IAAI,CAAA;IACvC,EAAE,CAAC,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;IAC9B,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,SAAS,CAAa,CAAA;IACrE,MAAM,EAAE,GAAG,SAAS,CAAC,cAAc,EAAE,CAAC,CAAC,CAAA;IAEvC,OAAO,CAAC,KAAK,CAAC,wBAAwB,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA;IAC7D,OAAO,CAAC,GAAG,CAAC,wBAAwB,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAA,CAAC,iCAAiC;IAC7F,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;AACrB,CAAC"}

package/package.json

@@ -1,7 +1,8 @@
 {
   "name": "@jbrowse/img",
-  "version": "2.2.0",
-  "main": "index.js",
+  "version": "2.2.2",
+  "main": "dist/index.js",
+  "module": "esm/index.js",
   "author": "JBrowse Team",
   "license": "Apache-2.0",
   "engines": {
@@ -11,21 +12,25 @@
     "jb2export": "./dist/bin.js"
   },
   "files": [
-    "dist"
+    "dist",
+    "esm",
+    "src"
   ],
   "scripts": {
-    "pretest": "cd ../jbrowse-react-linear-genome-view; yarn build; cd ../jb2export",
-    "test": "jest",
-    "prebuild": "rm -rf dist",
-    "build": "babel --root-mode upward src -d dist",
+    "test": "cd ../../; jest --env node --testMatch '**/*testmod.js' products/jbrowse-img",
+    "clean": "rm -rf dist esm *.tsbuildinfo",
+    "prebuild": "yarn clean",
+    "build": "npm-run-all build:*",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
     "preversion": "npm run build"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
     "@emotion/cache": "^11.7.1",
     "@emotion/react": "^11.9.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.2.0",
-    "@jbrowse/react-linear-genome-view": "^2.2.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.2.2",
+    "@jbrowse/react-linear-genome-view": "^2.2.2",
     "abortcontroller-polyfill": "^1.7.3",
     "canvas": "^2.9.1",
     "jsdom": "^19.0.0",
@@ -39,5 +44,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
+  "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
 }

package/src/bin.js

@@ -0,0 +1,2 @@
+#!/usr/bin/env node
+require('./index.js')

package/src/index.test.js

@@ -0,0 +1,179 @@
+/**
+ * @jest-environment node
+ */
+
+// the above jest-environment node is important to check true usage as a CLI tool
+
+import { renderRegion } from './renderRegion'
+import path from 'path'
+import fs from 'fs'
+import { JSDOM } from 'jsdom'
+import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
+import { Image, createCanvas } from 'canvas'
+import fetch, { Headers, Response, Request } from 'node-fetch'
+
+global.fetch = fetch
+global.Headers = Headers
+global.Response = Response
+global.Request = Request
+
+const { document } = new JSDOM(`...`).window
+global.document = document
+global.nodeImage = Image
+global.nodeCreateCanvas = createCanvas
+
+xtest('renders a region with --session and --config args', async () => {
+  const result = await renderRegion({
+    session: path.join(__dirname, '../test/clingen_session.json'),
+    config: path.join(__dirname, '../data/config.json'),
+  })
+  fs.writeFileSync('svg_from_config_and_session_param.svg', result)
+  expect(result).toMatchSnapshot()
+}, 40000)
+
+xtest('renders a region with --session, --tracks, and --assembly args', async () => {
+  const result = await renderRegion({
+    session: path.join(__dirname, '../test/clingen_session.json'),
+    tracks: path.join(__dirname, '../data/tracks.json'),
+    assembly: path.join(__dirname, '../data/assembly.json'),
+  })
+  fs.writeFileSync('svg_from_separate_session_and_tracks.svg', result)
+  expect(result).toMatchSnapshot()
+}, 40000)
+
+test('renders volvox with variety of args', async () => {
+  const fp = f => path.join(__dirname, '../data/volvox/' + f)
+  console.error = jest.fn()
+  const result = await renderRegion({
+    fasta: fp('volvox.fa'),
+    trackList: [
+      ['bam', [fp('volvox-sorted.bam')]],
+      ['cram', [fp('volvox-sorted.cram')]],
+      ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
+      ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
+      ['gffgz', [fp('volvox.sort.gff3.gz')]],
+      ['bigbed', [fp('volvox.bb')]],
+      ['bedgz', [fp('volvox-bed12.bed.gz')]],
+    ],
+    loc: 'ctgA:1000-2000',
+  })
+  fs.writeFileSync(
+    path.join(__dirname, '../test/svg_from_volvox_fasta_and_bam.svg'),
+    result,
+  )
+  expect(result).toBeTruthy()
+}, 40000)
+
+xtest('renders human large region with remote urls', async () => {
+  const result = await renderRegion({
+    fasta: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz',
+    trackList: [
+      [
+        'cram',
+        [
+          'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/skbr3.ont.sort.mod.cram',
+          'force:true',
+        ],
+      ],
+    ],
+    loc: '1:10,000,000-10,030,000',
+  })
+  fs.writeFileSync(
+    path.join(__dirname, '../test/human_remote_urls_large_region.svg'),
+    result,
+  )
+  expect(result).toBeTruthy()
+}, 120000)
+
+xtest('renders volvox with remote urls', async () => {
+  const result = await renderRegion({
+    fasta: 'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox.fa',
+    trackList: [
+      [
+        'bam',
+        [
+          'https://jbrowse.org/code/jb2/main/test_data/volvox/volvox-sorted.bam',
+        ],
+      ],
+    ],
+    loc: 'ctgA:1-1000',
+  })
+  fs.writeFileSync(
+    path.join(__dirname, '../test/volvox_remote_region.svg'),
+    result,
+  )
+  expect(result).toBeTruthy()
+}, 20000)
+
+test('renders volvox with variety of args (noRasterize)', async () => {
+  const fp = f => path.join(__dirname, '../data/volvox/' + f)
+  console.error = jest.fn()
+  const result = await renderRegion({
+    fasta: fp('volvox.fa'),
+    trackList: [
+      ['bam', [fp('volvox-sorted.bam')]],
+      ['cram', [fp('volvox-sorted.cram')]],
+      ['bigwig', [fp('volvox-sorted.bam.coverage.bw')]],
+      ['vcfgz', [fp('volvox.filtered.vcf.gz')]],
+      ['gffgz', [fp('volvox.sort.gff3.gz')]],
+      ['bigbed', [fp('volvox.bb')]],
+      ['bedgz', [fp('volvox-bed12.bed.gz')]],
+    ],
+    loc: 'ctgA:1000-2000',
+    noRasterize: true,
+  })
+  fs.writeFileSync(
+    path.join(
+      __dirname,
+      '../test/svg_from_volvox_fasta_and_bam_norasterize.svg',
+    ),
+    result,
+  )
+  expect(result).toBeTruthy()
+}, 40000)
+
+// commented out for using remote files currently
+xtest('configtracks arg with urls', async () => {
+  const result = await renderRegion({
+    config: 'data/config.json',
+    trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
+    assembly: 'GRCh38',
+    loc: 'chr1:50,000-60,000',
+  })
+  fs.writeFileSync('svg_configtracks_simple.svg', result)
+  expect(result).toBeTruthy()
+}, 40000)
+
+test('configtracks arg with local files', async () => {
+  const result = await renderRegion({
+    config: path.join(__dirname, '../data/volvox/config.json'),
+    trackList: [['configtracks', ['volvox_sv']]],
+    assembly: 'volvox',
+    loc: 'ctgA:1-50,000',
+  })
+  fs.writeFileSync(
+    path.join(__dirname, '../test/svg_configtracks_local.svg'),
+    result,
+  )
+  expect(result).toBeTruthy()
+}, 40000)
+
+xtest('renders --hic', async () => {
+  const result = await renderRegion({
+    fasta: 'https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz',
+    trackList: [
+      [
+        'hic',
+        [
+          'https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic',
+        ],
+      ],
+    ],
+    loc: '1:2,000,000-10,000,000',
+  })
+  fs.writeFileSync(
+    path.join(__dirname, '../test/svg_from_human_hic.svg'),
+    result,
+  )
+  expect(result).toBeTruthy()
+}, 20000)