@jbrowse/img 1.7.7 → 1.7.10

package/README.md

@@ -10,7 +10,7 @@ You don't need to have JBrowse 2 installed to use this tool. The tool can genera
 
 ## Screenshot
 
-![](img/1.png)
+![](https://raw.githubusercontent.com/GMOD/jbrowse-components/main/products/jbrowse-img/img/1.png)
 
 More examples [EXAMPLES.md](EXAMPLES.md)
 
@@ -51,14 +51,21 @@ jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000
 
 If `--out` is not specified it writes to out.svg
 
-### Generate PDF of PNG instead of SVG
+### Generate PNG instead of SVG
 
-If a filename with a `pdf` or `png` extension is supplied to `--out` then the
-tool tries to convert from svg to pdf/png using rsvg-convert (you will need to
-install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`)
+Supply a file with the png extension to `--out`, uses rsvg-convert so you will
+need to install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`
 
 ```
 jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.png
+```
+
+### Generate PDF instead of SVG
+
+Supply a file with the pdf extension to `--out`, uses rsvg-convert so you will
+need to install rsvg-convert to your system e.g. with `sudo apt install librsvg2-bin`
+
+```
 jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.pdf
 ```
 
@@ -66,7 +73,7 @@ jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000
 
 This example shows using remote files, e.g. with human hg19 and several tracks
 
-Note the use of --aliases to smooth over refname differences e.g. fasta
+Note the use of --aliases, which smoothes over refname differences e.g. fasta
 contains 1 for chr1, and bigbed contains chr1, gff contains NC_000001.10
 
 ```

package/dist/index.js

@@ -24,11 +24,16 @@ var _child_process = require("child_process");
 
 var _nodeFetch = _interopRequireWildcard(require("node-fetch"));
 
+var _jsdom = require("jsdom");
+
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
 /* eslint-disable no-console */
+var document = new _jsdom.JSDOM("...").window.document;
+global.document = document;
+
 if (!global.fetch) {
   global.fetch = _nodeFetch.default;
   global.Headers = _nodeFetch.Headers;

package/dist/index.testmod.js

@@ -10,6 +10,13 @@ var _renderRegion = require("./renderRegion");
 
 var _fs = _interopRequireDefault(require("fs"));
 
+var _jsdom = require("jsdom");
+
+require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
+
+var document = new _jsdom.JSDOM("...").window.document;
+global.document = document;
+
 function hashCode(str) {
   var hash = 0;
   var chr;
@@ -84,20 +91,24 @@ xtest('renders a region with --session, --tracks, and --assembly args', /*#__PUR
   }, _callee2);
 })), timeout);
 test('renders volvox with variety of args', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-  var result;
+  var fp, result;
   return _regenerator.default.wrap(function _callee3$(_context3) {
     while (1) {
       switch (_context3.prev = _context3.next) {
         case 0:
+          fp = function fp(f) {
+            return require.resolve('../data/volvox/' + f);
+          };
+
           console.error = jest.fn();
-          _context3.next = 3;
+          _context3.next = 4;
           return (0, _renderRegion.renderRegion)({
-            fasta: require.resolve('../data/volvox/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')]]],
+            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'
           });
 
-        case 3:
+        case 4:
           result = _context3.sent;
 
           // can't do a snapshot test here, slightly inconsistent results(?)
@@ -105,21 +116,55 @@ test('renders volvox with variety of args', /*#__PURE__*/(0, _asyncToGenerator2.
 
           expect(result).toBeTruthy();
 
-        case 6:
+        case 7:
         case "end":
           return _context3.stop();
       }
     }
   }, _callee3);
+})), timeout);
+test('renders volvox with variety of args (noRasterize)', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
+  var fp, result;
+  return _regenerator.default.wrap(function _callee4$(_context4) {
+    while (1) {
+      switch (_context4.prev = _context4.next) {
+        case 0:
+          fp = function fp(f) {
+            return require.resolve('../data/volvox/' + f);
+          };
+
+          console.error = jest.fn();
+          _context4.next = 4;
+          return (0, _renderRegion.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
+          });
+
+        case 4:
+          result = _context4.sent;
+
+          // can't do a snapshot test here, slightly inconsistent results(?)
+          _fs.default.writeFileSync(require.resolve('../test/svg_from_volvox_fasta_and_bam_norasterize.svg'), result);
+
+          expect(result).toBeTruthy();
+
+        case 7:
+        case "end":
+          return _context4.stop();
+      }
+    }
+  }, _callee4);
 })), timeout); // commented out for using remote files currently
 
-xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
+xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
   var result;
-  return _regenerator.default.wrap(function _callee4$(_context4) {
+  return _regenerator.default.wrap(function _callee5$(_context5) {
     while (1) {
-      switch (_context4.prev = _context4.next) {
+      switch (_context5.prev = _context5.next) {
         case 0:
-          _context4.next = 2;
+          _context5.next = 2;
           return (0, _renderRegion.renderRegion)({
             config: 'data/config.json',
             trackList: [['configtracks', ['ncbi_refseq_109_hg38']]],
@@ -128,7 +173,7 @@ xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)
           });
 
         case 2:
-          result = _context4.sent;
+          result = _context5.sent;
 
           // can't do a snapshot test here, slightly inconsistent results(?)
           _fs.default.writeFileSync('svg_configtracks_simple.svg', result);
@@ -137,18 +182,18 @@ xtest('configtracks arg with urls', /*#__PURE__*/(0, _asyncToGenerator2.default)
 
         case 5:
         case "end":
-          return _context4.stop();
+          return _context5.stop();
       }
     }
-  }, _callee4);
+  }, _callee5);
 })), timeout * 3);
-test('configtracks arg with local files', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5() {
+test('configtracks arg with local files', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6() {
   var result;
-  return _regenerator.default.wrap(function _callee5$(_context5) {
+  return _regenerator.default.wrap(function _callee6$(_context6) {
     while (1) {
-      switch (_context5.prev = _context5.next) {
+      switch (_context6.prev = _context6.next) {
         case 0:
-          _context5.next = 2;
+          _context6.next = 2;
           return (0, _renderRegion.renderRegion)({
             config: require.resolve('../data/volvox/config.json'),
             trackList: [['configtracks', ['volvox_sv']]],
@@ -157,7 +202,7 @@ test('configtracks arg with local files', /*#__PURE__*/(0, _asyncToGenerator2.de
           });
 
         case 2:
-          result = _context5.sent;
+          result = _context6.sent;
 
           // can't do a snapshot test here, slightly inconsistent results(?)
           _fs.default.writeFileSync(require.resolve('../test/svg_configtracks_local.svg'), result);
@@ -166,18 +211,18 @@ test('configtracks arg with local files', /*#__PURE__*/(0, _asyncToGenerator2.de
 
         case 5:
         case "end":
-          return _context5.stop();
+          return _context6.stop();
       }
     }
-  }, _callee5);
+  }, _callee6);
 })), timeout * 3);
-xtest('renders --hic', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6() {
+xtest('renders --hic', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7() {
   var result;
-  return _regenerator.default.wrap(function _callee6$(_context6) {
+  return _regenerator.default.wrap(function _callee7$(_context7) {
     while (1) {
-      switch (_context6.prev = _context6.next) {
+      switch (_context7.prev = _context7.next) {
         case 0:
-          _context6.next = 2;
+          _context7.next = 2;
           return (0, _renderRegion.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']]],
@@ -185,7 +230,7 @@ xtest('renders --hic', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__
           });
 
         case 2:
-          result = _context6.sent;
+          result = _context7.sent;
 
           _fs.default.writeFileSync(require.resolve('../test/svg_from_human_hic.svg'), result);
 
@@ -193,8 +238,8 @@ xtest('renders --hic', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__
 
         case 5:
         case "end":
-          return _context6.stop();
+          return _context7.stop();
       }
     }
-  }, _callee6);
+  }, _callee7);
 })), 20000);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/img",
-  "version": "1.7.7",
+  "version": "1.7.10",
   "main": "index.js",
   "author": "JBrowse Team",
   "license": "Apache-2.0",
@@ -29,9 +29,10 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "@jbrowse/plugin-linear-genome-view": "^1.7.7",
-    "@jbrowse/react-linear-genome-view": "^1.7.7",
+    "@jbrowse/plugin-linear-genome-view": "^1.7.10",
+    "@jbrowse/react-linear-genome-view": "^1.7.10",
     "abortcontroller-polyfill": "^1.7.3",
+    "jsdom": "^19.0.0",
     "mobx": "^5.10.1",
     "node-fetch": "^2.6.7",
     "react": "^17.0.1",
@@ -42,5 +43,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "2c26e04ae942c380bf2f5b79ef7a49cc32b7bfed"
+  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
 }