Add jsdom to jbrowse-img to fix --noRasterize option (#3009)

* Add jsdom for noRasterize

* Use plain node instead of jsdom environment when testing jbrowse/img

package.json

@@ -18,7 +18,7 @@
     "check-format": "prettier --check .",
     "typecheck": "tsc --noEmit",
     "pretest-ci": "cd products/jbrowse-react-linear-genome-view;yarn build;cd ../../",
-    "test-ci": "cross-env NODE_OPTIONS='--max-old-space-size=7000' jest --ci --coverage && jest --testMatch '**/*testmod.js'",
+    "test-ci": "cross-env NODE_OPTIONS='--max-old-space-size=7000' jest --ci --coverage && jest --env node --testMatch '**/*testmod.js'",
     "built-test-ci": "jest --ci integration.test.js",
     "test": "jest"
   },

products/jbrowse-img/package.json

@@ -32,6 +32,7 @@
     "@jbrowse/plugin-linear-genome-view": "^1.7.9",
     "@jbrowse/react-linear-genome-view": "^1.7.9",
     "abortcontroller-polyfill": "^1.7.3",
+    "jsdom": "^19.0.0",
     "mobx": "^5.10.1",
     "node-fetch": "^2.6.7",
     "react": "^17.0.1",

products/jbrowse-img/src/index.js

@@ -7,6 +7,10 @@ import tmp from 'tmp'
 import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
 import { spawnSync } from 'child_process'
 import fetch, { Headers, Response, Request } from 'node-fetch'
+import { JSDOM } from 'jsdom'
+
+const { document } = new JSDOM(`...`).window
+global.document = document
 
 if (!global.fetch) {
   global.fetch = fetch

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

@@ -1,5 +1,10 @@
 import { renderRegion } from './renderRegion'
 import fs from 'fs'
+import { JSDOM } from 'jsdom'
+import 'abortcontroller-polyfill/dist/abortcontroller-polyfill-only'
+
+const { document } = new JSDOM(`...`).window
+global.document = document
 
 function hashCode(str) {
   let hash = 0
@@ -49,20 +54,18 @@ xtest(
 test(
   'renders volvox with variety of args',
   async () => {
+    const fp = f => require.resolve('../data/volvox/' + f)
     console.error = jest.fn()
     const result = await renderRegion({
-      fasta: require.resolve('../data/volvox/volvox.fa'),
+      fasta: fp('volvox.fa'),
       trackList: [
-        ['bam', [require.resolve('../data/volvox/volvox-sorted.bam')]],
-        ['cram', [require.resolve('../data/volvox/volvox-sorted.cram')]],
-        [
-          'bigwig',
-          [require.resolve('../data/volvox/volvox-sorted.bam.coverage.bw')],
-        ],
-        ['vcfgz', [require.resolve('../data/volvox/volvox.filtered.vcf.gz')]],
-        ['gffgz', [require.resolve('../data/volvox/volvox.sort.gff3.gz')]],
-        ['bigbed', [require.resolve('../data/volvox/volvox.bb')]],
-        ['bedgz', [require.resolve('../data/volvox/volvox-bed12.bed.gz')]],
+        ['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',
     })
@@ -76,6 +79,35 @@ test(
   timeout,
 )
 
+test(
+  'renders volvox with variety of args (noRasterize)',
+  async () => {
+    const fp = f => require.resolve('../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,
+    })
+    // can't do a snapshot test here, slightly inconsistent results(?)
+    fs.writeFileSync(
+      require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'),
+      result,
+    )
+    expect(result).toBeTruthy()
+  },
+  timeout,
+)
+
 // commented out for using remote files currently
 xtest(
   'configtracks arg with urls',

yarn.lock

@@ -5174,7 +5174,7 @@ JSONStream@^1.0.4:
     jsonparse "^1.2.0"
     through ">=2.2.7 <3"
 
-abab@^2.0.3, abab@^2.0.5:
+abab@^2.0.3, abab@^2.0.5, abab@^2.0.6:
   version "2.0.6"
   resolved "https://registry.yarnpkg.com/abab/-/abab-2.0.6.tgz#41b80f2c871d19686216b82309231cfd3cb3d291"
   integrity sha512-j2afSsaIENvHZN2B8GOpF566vZ5WVk5opAiMTvWgaQT8DkbOqsTfvNAvHoRGU2zzP8cPoqys+xHTRDWW8L+/BA==
@@ -7870,6 +7870,11 @@ cssom@^0.4.4:
   resolved "https://registry.yarnpkg.com/cssom/-/cssom-0.4.4.tgz#5a66cf93d2d0b661d80bf6a44fb65f5c2e4e0a10"
   integrity sha512-p3pvU7r1MyyqbTk+WbNJIgJjG2VmTIaB10rI93LzVPrmDJKkzKYMtxxyAvQXR/NS6otuzveI7+7BBq3SjBS2mw==
 
+cssom@^0.5.0:
+  version "0.5.0"
+  resolved "https://registry.yarnpkg.com/cssom/-/cssom-0.5.0.tgz#d254fa92cd8b6fbd83811b9fbaed34663cc17c36"
+  integrity sha512-iKuQcq+NdHqlAcwUY0o/HL69XQrUaQdMjmStJ8JFmUaiiQErlhrmuigkg/CU4E2J0IyUKUrMAgl36TvN67MqTw==
+
 cssom@~0.3.6:
   version "0.3.8"
   resolved "https://registry.yarnpkg.com/cssom/-/cssom-0.3.8.tgz#9f1276f5b2b463f2114d3f2c75250af8c1a36f4a"
@@ -7983,6 +7988,15 @@ data-urls@^2.0.0:
     whatwg-mimetype "^2.3.0"
     whatwg-url "^8.0.0"
 
+data-urls@^3.0.1:
+  version "3.0.2"
+  resolved "https://registry.yarnpkg.com/data-urls/-/data-urls-3.0.2.tgz#9cf24a477ae22bcef5cd5f6f0bfbc1d2d3be9143"
+  integrity sha512-Jy/tj3ldjZJo63sVAvg6LHt2mHvl4V6AgRAmNDtLdm7faqtsx+aJG42rsyCo9JCoRVKwPFzKlIPx3DIibwSIaQ==
+  dependencies:
+    abab "^2.0.6"
+    whatwg-mimetype "^3.0.0"
+    whatwg-url "^11.0.0"
+
 date-fns@^2.16.1:
   version "2.28.0"
   resolved "https://registry.yarnpkg.com/date-fns/-/date-fns-2.28.0.tgz#9570d656f5fc13143e50c975a3b6bbeb46cd08b2"
@@ -8037,7 +8051,7 @@ decamelize@^1.1.0, decamelize@^1.1.2:
   resolved "https://registry.yarnpkg.com/decamelize/-/decamelize-1.2.0.tgz#f6534d15148269b20352e7bee26f501f9a191290"
   integrity sha512-z2S+W9X73hAUUki+N+9Za2lBlun89zigOyGrsax+KUQ6wKW4ZoWpEYBkGhQjwAjjDCkWxhY0VKEhk8wzY7F5cA==
 
-decimal.js@^10.2.1:
+decimal.js@^10.2.1, decimal.js@^10.3.1:
   version "10.3.1"
   resolved "https://registry.yarnpkg.com/decimal.js/-/decimal.js-10.3.1.tgz#d8c3a444a9c6774ba60ca6ad7261c3a94fd5e783"
   integrity sha512-V0pfhfr8suzyPGOx3nmq4aHqabehUZn6Ch9kyFpV79TGDTWFmHqUqXdabR7QHqxzrYolF4+tVmJhUG4OURg5dQ==
@@ -8461,6 +8475,13 @@ domexception@^2.0.1:
   dependencies:
     webidl-conversions "^5.0.0"
 
+domexception@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/domexception/-/domexception-4.0.0.tgz#4ad1be56ccadc86fc76d033353999a8037d03673"
+  integrity sha512-A2is4PLG+eeSfoTMA95/s4pvAoSo2mKtiM5jlHkAVewmiO8ISFTFKZjH7UAM1Atli/OT/7JHOrJRJiMKUZKYBw==
+  dependencies:
+    webidl-conversions "^7.0.0"
+
 domhandler@^4.0.0, domhandler@^4.2.0, domhandler@^4.3.1:
   version "4.3.1"
   resolved "https://registry.yarnpkg.com/domhandler/-/domhandler-4.3.1.tgz#8d792033416f59d68bc03a5aa7b018c1ca89279c"
@@ -10726,6 +10747,13 @@ html-encoding-sniffer@^2.0.1:
   dependencies:
     whatwg-encoding "^1.0.5"
 
+html-encoding-sniffer@^3.0.0:
+  version "3.0.0"
+  resolved "https://registry.yarnpkg.com/html-encoding-sniffer/-/html-encoding-sniffer-3.0.0.tgz#2cb1a8cf0db52414776e5b2a7a04d5dd98158de9"
+  integrity sha512-oWv4T4yJ52iKrufjnyZPkrN0CH3QnrUqdB6In1g5Fe1mia8GmF36gnfNySxoZtxD5+NmYw1EElVXiBk93UeskA==
+  dependencies:
+    whatwg-encoding "^2.0.0"
+
 html-entities@^2.1.0, html-entities@^2.3.2:
   version "2.3.3"
   resolved "https://registry.yarnpkg.com/html-entities/-/html-entities-2.3.3.tgz#117d7626bece327fc8baace8868fa6f5ef856e46"
@@ -10980,7 +11008,7 @@ iconv-lite@0.4.24, iconv-lite@^0.4.24:
   dependencies:
     safer-buffer ">= 2.1.2 < 3"
 
-iconv-lite@^0.6.2, iconv-lite@^0.6.3:
+iconv-lite@0.6.3, iconv-lite@^0.6.2, iconv-lite@^0.6.3:
   version "0.6.3"
   resolved "https://registry.yarnpkg.com/iconv-lite/-/iconv-lite-0.6.3.tgz#a52f80bf38da1952eb5c681790719871a1a72501"
   integrity sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw==
@@ -12464,6 +12492,39 @@ jsdom@^16.6.0:
     ws "^7.4.6"
     xml-name-validator "^3.0.0"
 
+jsdom@^19.0.0:
+  version "19.0.0"
+  resolved "https://registry.yarnpkg.com/jsdom/-/jsdom-19.0.0.tgz#93e67c149fe26816d38a849ea30ac93677e16b6a"
+  integrity sha512-RYAyjCbxy/vri/CfnjUWJQQtZ3LKlLnDqj+9XLNnJPgEGeirZs3hllKR20re8LUZ6o1b1X4Jat+Qd26zmP41+A==
+  dependencies:
+    abab "^2.0.5"
+    acorn "^8.5.0"
+    acorn-globals "^6.0.0"
+    cssom "^0.5.0"
+    cssstyle "^2.3.0"
+    data-urls "^3.0.1"
+    decimal.js "^10.3.1"
+    domexception "^4.0.0"
+    escodegen "^2.0.0"
+    form-data "^4.0.0"
+    html-encoding-sniffer "^3.0.0"
+    http-proxy-agent "^5.0.0"
+    https-proxy-agent "^5.0.0"
+    is-potential-custom-element-name "^1.0.1"
+    nwsapi "^2.2.0"
+    parse5 "6.0.1"
+    saxes "^5.0.1"
+    symbol-tree "^3.2.4"
+    tough-cookie "^4.0.0"
+    w3c-hr-time "^1.0.2"
+    w3c-xmlserializer "^3.0.0"
+    webidl-conversions "^7.0.0"
+    whatwg-encoding "^2.0.0"
+    whatwg-mimetype "^3.0.0"
+    whatwg-url "^10.0.0"
+    ws "^8.2.3"
+    xml-name-validator "^4.0.0"
+
 jsesc@^2.5.1:
   version "2.5.2"
   resolved "https://registry.yarnpkg.com/jsesc/-/jsesc-2.5.2.tgz#80564d2e483dacf6e8ef209650a67df3f0c283a4"
@@ -18426,6 +18487,13 @@ tr46@^2.1.0:
   dependencies:
     punycode "^2.1.1"
 
+tr46@^3.0.0:
+  version "3.0.0"
+  resolved "https://registry.yarnpkg.com/tr46/-/tr46-3.0.0.tgz#555c4e297a950617e8eeddef633c87d4d9d6cbf9"
+  integrity sha512-l7FvfAHlcmulp8kr+flpQZmVwtu7nfRV7NZujtN0OqES8EL4O4e0qqzL0DC5gAvx/ZC/9lk6rhcUwYvkBnBnYA==
+  dependencies:
+    punycode "^2.1.1"
+
 tr46@~0.0.3:
   version "0.0.3"
   resolved "https://registry.yarnpkg.com/tr46/-/tr46-0.0.3.tgz#8184fd347dac9cdc185992f3a6622e14b9d9ab6a"
@@ -19108,6 +19176,13 @@ w3c-xmlserializer@^2.0.0:
   dependencies:
     xml-name-validator "^3.0.0"
 
+w3c-xmlserializer@^3.0.0:
+  version "3.0.0"
+  resolved "https://registry.yarnpkg.com/w3c-xmlserializer/-/w3c-xmlserializer-3.0.0.tgz#06cdc3eefb7e4d0b20a560a5a3aeb0d2d9a65923"
+  integrity sha512-3WFqGEgSXIyGhOmAFtlicJNMjEps8b1MG31NCA0/vOF9+nKMUW1ckhi9cnNHmf88Rzw5V+dwIwsm2C7X8k9aQg==
+  dependencies:
+    xml-name-validator "^4.0.0"
+
 wait-on@^6.0.0:
   version "6.0.1"
   resolved "https://registry.yarnpkg.com/wait-on/-/wait-on-6.0.1.tgz#16bbc4d1e4ebdd41c5b4e63a2e16dbd1f4e5601e"
@@ -19189,6 +19264,11 @@ webidl-conversions@^6.1.0:
   resolved "https://registry.yarnpkg.com/webidl-conversions/-/webidl-conversions-6.1.0.tgz#9111b4d7ea80acd40f5270d666621afa78b69514"
   integrity sha512-qBIvFLGiBpLjfwmYAaHPXsn+ho5xZnGvyGvsarywGNc8VyQJUMHJ8OBKGGrPER0okBeMDaan4mNBlgBROxuI8w==
 
+webidl-conversions@^7.0.0:
+  version "7.0.0"
+  resolved "https://registry.yarnpkg.com/webidl-conversions/-/webidl-conversions-7.0.0.tgz#256b4e1882be7debbf01d05f0aa2039778ea080a"
+  integrity sha512-VwddBukDzu71offAQR975unBIGqfKZpM+8ZX6ySk8nYhVoo5CYaZyzt3YBvYtRtO+aoGlqxPg/B87NGVZ/fu6g==
+
 webpack-cli@^4.9.1:
   version "4.9.2"
   resolved "https://registry.yarnpkg.com/webpack-cli/-/webpack-cli-4.9.2.tgz#77c1adaea020c3f9e2db8aad8ea78d235c83659d"
@@ -19405,6 +19485,13 @@ whatwg-encoding@^1.0.5:
   dependencies:
     iconv-lite "0.4.24"
 
+whatwg-encoding@^2.0.0:
+  version "2.0.0"
+  resolved "https://registry.yarnpkg.com/whatwg-encoding/-/whatwg-encoding-2.0.0.tgz#e7635f597fd87020858626805a2729fa7698ac53"
+  integrity sha512-p41ogyeMUrw3jWclHWTQg1k05DSVXPLcVxRTYsXUk+ZooOCZLcoYgPZ/HL/D/N+uQPOtcp1me1WhBEaX02mhWg==
+  dependencies:
+    iconv-lite "0.6.3"
+
 whatwg-fetch@^3.6.2:
   version "3.6.2"
   resolved "https://registry.yarnpkg.com/whatwg-fetch/-/whatwg-fetch-3.6.2.tgz#dced24f37f2624ed0281725d51d0e2e3fe677f8c"
@@ -19415,6 +19502,27 @@ whatwg-mimetype@^2.3.0:
   resolved "https://registry.yarnpkg.com/whatwg-mimetype/-/whatwg-mimetype-2.3.0.tgz#3d4b1e0312d2079879f826aff18dbeeca5960fbf"
   integrity sha512-M4yMwr6mAnQz76TbJm914+gPpB/nCwvZbJU28cUD6dR004SAxDLOOSUaB1JDRqLtaOV/vi0IC5lEAGFgrjGv/g==
 
+whatwg-mimetype@^3.0.0:
+  version "3.0.0"
+  resolved "https://registry.yarnpkg.com/whatwg-mimetype/-/whatwg-mimetype-3.0.0.tgz#5fa1a7623867ff1af6ca3dc72ad6b8a4208beba7"
+  integrity sha512-nt+N2dzIutVRxARx1nghPKGv1xHikU7HKdfafKkLNLindmPU/ch3U31NOCGGA/dmPcmb1VlofO0vnKAcsm0o/Q==
+
+whatwg-url@^10.0.0:
+  version "10.0.0"
+  resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-10.0.0.tgz#37264f720b575b4a311bd4094ed8c760caaa05da"
+  integrity sha512-CLxxCmdUby142H5FZzn4D8ikO1cmypvXVQktsgosNy4a4BHrDHeciBBGZhb0bNoR5/MltoCatso+vFjjGx8t0w==
+  dependencies:
+    tr46 "^3.0.0"
+    webidl-conversions "^7.0.0"
+
+whatwg-url@^11.0.0:
+  version "11.0.0"
+  resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-11.0.0.tgz#0a849eebb5faf2119b901bb76fd795c2848d4018"
+  integrity sha512-RKT8HExMpoYx4igMiVMY83lN6UeITKJlBQ+vR/8ZJ8OCdSiN3RwCq+9gH0+Xzj0+5IrM6i4j/6LuvzbZIQgEcQ==
+  dependencies:
+    tr46 "^3.0.0"
+    webidl-conversions "^7.0.0"
+
 whatwg-url@^5.0.0:
   version "5.0.0"
   resolved "https://registry.yarnpkg.com/whatwg-url/-/whatwg-url-5.0.0.tgz#966454e8765462e37644d3626f6742ce8b70965d"
@@ -19795,6 +19903,11 @@ xml-name-validator@^3.0.0:
   resolved "https://registry.yarnpkg.com/xml-name-validator/-/xml-name-validator-3.0.0.tgz#6ae73e06de4d8c6e47f9fb181f78d648ad457c6a"
   integrity sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw==
 
+xml-name-validator@^4.0.0:
+  version "4.0.0"
+  resolved "https://registry.yarnpkg.com/xml-name-validator/-/xml-name-validator-4.0.0.tgz#79a006e2e63149a8600f15430f0a4725d1524835"
+  integrity sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==
+
 xmlbuilder@>=11.0.1:
   version "15.1.1"
   resolved "https://registry.yarnpkg.com/xmlbuilder/-/xmlbuilder-15.1.1.tgz#9dcdce49eea66d8d10b42cae94a79c3c8d0c2ec5"