@jbrowse/img 1.7.9 → 2.0.0

package/README.md

@@ -29,8 +29,6 @@ guide](DEVELOPER.md) for details
 
 ## Example usages
 
-This will show some example usages
-
 ### Use with local files
 
 We can call this script on local files, and it doesn't require a web browser,
@@ -56,7 +54,7 @@ If `--out` is not specified it writes to out.svg
 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`
 
-```
+```bash
 jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.png
 ```
 
@@ -65,7 +63,7 @@ jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000
 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`
 
-```
+```bash
 jb2export --fasta yourfile.fa --bam yourfile.bam --loc chr1:1,000,000-1,001,000 --out file.pdf
 ```
 
@@ -76,8 +74,7 @@ This example shows using remote files, e.g. with human hg19 and several tracks
 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
 
-```
-
+```bash
 jb2export --fasta https://jbrowse.org/genomes/hg19/fasta/hg19.fa.gz \
   --aliases https://jbrowse.org/genomes/hg19/hg19_aliases.txt  \
   --bigbed https://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/clinvar/clinvarMain.bb \
@@ -158,7 +155,7 @@ If you use jbrowse-web, you can select File->Export session which produces a
 session.json file, and then use the --session parameter. Make sure to specify
 the assembly also, it currently does not infer the assembly from the session
 
-```
+```bash
 jb2export --config data/skbr3/config.json \
   --session session.json \
   --assembly hg19
@@ -210,7 +207,7 @@ Then you can call it like above
 
 ```bash
 jb2export --config data/volvox/config.json \
-  --assembly volvox
+  --assembly volvox \
   --configtracks volvox_sv \
   --loc ctgA:1-50,000
 ```
@@ -340,10 +337,6 @@ convert -size 2048x out.svg out.png
 
 ## Troubleshooting
 
-### I see the message 'useLayoutEffect does nothing on the server'
-
-This is a harmless warning, we are working on fixing it though
-
 ### I don't get any outputted svg and no message
 
 The error reporting from the app is not very good at the moment so often has
@@ -357,8 +350,3 @@ There are some new features in the latest NPM (2021, v7) related to
 peerDependencies that may produce some warnings. It should work even despite
 making warnings, but you can use yarn to install or use legacy peer
 dependencies if you want to avoid install time warningsvg
-
-### The program keeps running after saying it completed?
-
-We are looking into this still. The file should have been generated though, and
-the program will complete

package/dist/index.js

@@ -24,11 +24,20 @@ var _child_process = require("child_process");
 
 var _nodeFetch = _interopRequireWildcard(require("node-fetch"));
 
+var _jsdom = require("jsdom");
+
+var _canvas = require("canvas");
+
 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 */
+global.nodeImage = _canvas.Image;
+global.nodeCreateCanvas = _canvas.createCanvas;
+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 +10,17 @@ var _renderRegion = require("./renderRegion");
 
 var _fs = _interopRequireDefault(require("fs"));
 
+var _jsdom = require("jsdom");
+
+require("abortcontroller-polyfill/dist/abortcontroller-polyfill-only");
+
+var _canvas = require("canvas");
+
+var document = new _jsdom.JSDOM("...").window.document;
+global.document = document;
+global.nodeImage = _canvas.Image;
+global.nodeCreateCanvas = _canvas.createCanvas;
+
 function hashCode(str) {
   var hash = 0;
   var chr;
@@ -84,20 +95,24 @@ 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 +120,55 @@ 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 +177,7 @@ 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 +186,18 @@ 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 +206,7 @@ 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 +215,18 @@ 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 +234,7 @@ 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 +242,8 @@ 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": "1.7.9",
+  "version": "2.0.0",
   "main": "index.js",
   "author": "JBrowse Team",
   "license": "Apache-2.0",
@@ -29,18 +29,20 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
-    "@jbrowse/plugin-linear-genome-view": "^1.7.9",
-    "@jbrowse/react-linear-genome-view": "^1.7.9",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@jbrowse/react-linear-genome-view": "^2.0.0",
     "abortcontroller-polyfill": "^1.7.3",
-    "mobx": "^5.10.1",
+    "canvas": "^2.9.1",
+    "jsdom": "^19.0.0",
+    "mobx": "^6.6.0",
     "node-fetch": "^2.6.7",
-    "react": "^17.0.1",
-    "react-dom": "^17.0.1",
+    "react": "^17.0.0",
+    "react-dom": "^17.0.0",
     "tmp": "^0.2.1",
     "yargs": "^17.3.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "a6504c385d703ce6e755d05652ef659ffe28c864"
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }