Merge db8a39b into a02c908

.flowconfig

@@ -2,6 +2,7 @@
 .*node_modules/flow-bin.*
 .*node_modules/jsxhint.*
 .*node_modules/.*mocha.*
+.*node_modules/reactify.*
 .*build.*
 
 [include]

.jshintrc

@@ -0,0 +1,11 @@
+{
+  "node": true,  // allow "require", "module.exports", etc.
+  "browser": true,  // allow document, window, console, etc.
+  "lastsemic": true,  // allow missing semicolons in one-liners
+  "unused": "vars",  // unused vars are bad, but function params are OK
+  "undef": true,  // catch use before define errors
+  "globalstrict": true,  // allow module-level "use strict", which is OK with browserify.
+  "laxbreak": true,  // allow ambiguous continuation lines, e.g. "+" on next line
+  "esnext": true,  // allow ES6 features
+  "mocha": true  // allow "describe", "it" and friends
+}

.travis.yml

@@ -5,4 +5,4 @@ node_js:
 
 before_install: npm install -g grunt-cli
 
-script: grunt travis && ./scripts/post-coverage.sh
+script: grunt travis && ./scripts/lint.sh && ./scripts/post-coverage.sh

Gruntfile.js

@@ -52,7 +52,10 @@ module.exports = function(grunt) {
             "reactify",
             {
               harmony: true,
-              stripTypes: true
+              stripTypes: true,
+              reactOptions: {
+                nonStrictEs6module: true
+              }
             }
           ]
         ],

package.json

@@ -7,6 +7,10 @@
     "type": "git",
     "url": "https://github.com/danvk/pileup.js.git"
   },
+  "scripts": {
+    "lint": "./scripts/lint.sh",
+    "test": "grunt test"
+  },
   "author": "Dan Vanderkam",
   "license": "Apache2",
   "bugs": {
@@ -39,12 +43,13 @@
     "grunt-jscoverage": "^0.1.3",
     "grunt-mocha-phantomjs": ">=0.6.1",
     "grunt-mocha-test": "^0.12.7",
+    "jsxhint": "git://github.com/danvk/JSXHint#nonStrictEs6module",
     "lcov-parse": "0.0.9",
     "mocha": "^2.1.0",
     "mocha-lcov-reporter": ">=0.0.2",
     "parse-data-uri": "^0.2.0",
     "react-tools": "^0.13.1",
-    "reactify": "^1.0.0",
+    "reactify": "danvk/reactify",
     "sinon": "^1.12.2",
     "source-map": "^0.3.0"
   }

scripts/lint.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+./node_modules/.bin/jsxhint --es6module --harmony 'src/**/*.js' 'test/**/*.js'

src/BigBed.js

@@ -117,7 +117,7 @@ function attachContigToBedRows(beds, contigMap) {
 // Internal function for fetching features by block.
 function fetchFeaturesByBlock(contigRange, header, cirTree, remoteFile): Array<BedBlock> {
   var blocks = findOverlappingBlocks(header, cirTree, contigRange);
-  if (blocks.length == 0) {
+  if (blocks.length === 0) {
     return Q.when([]);
   }
 
@@ -240,7 +240,7 @@ class BigBed {
                     (header, cirTree, contigMap) => {
       var contigIx = getContigId(contigMap, range.contig);
       if (contigIx === null) {
-        throw `Invalid contig ${contig}`;
+        throw `Invalid contig ${range.contig}`;
       }
       var indexRange = new ContigInterval(contigIx, range.start(), range.stop());
       return fetchFeaturesByBlock(indexRange, header, cirTree, this.remoteFile)

src/BigBedDataSource.js

@@ -79,7 +79,7 @@ function createBigBedDataSource(remoteSource: BigBed): BigBedSource {
   var genes: {[key:string]: Gene} = {};
 
   // Ranges for which we have complete information -- no need to hit network.
-  var coveredRanges: Array<ContigInterval<string>> = []
+  var coveredRanges: Array<ContigInterval<string>> = [];
 
   function addGene(newGene) {
     if (!genes[newGene.id]) {

src/ContigInterval.js

@@ -1,4 +1,5 @@
 /* @flow */
+'use strict';
 
 var Interval = require('./Interval');
 

src/Controls.js

@@ -2,6 +2,7 @@
  * Controls for zooming to particular ranges of the genome.
  * @flow
  */
+'use strict';
 
 var React = require('react'),
     types = require('./types'),

src/GeneTrack.js

@@ -2,6 +2,8 @@
  * Visualization of genes, including exons and coding regions.
  * @flow
  */
+'use strict';
+
 var React = require('react/addons'),
     _ = require('underscore'),
     d3 = require('d3'),
@@ -39,7 +41,7 @@ var NonEmptyGeneTrack = React.createClass({
                 .append('svg');
 
     // These define the left/right arrow patterns for sense/antisense genes.
-    var defs = svg.append('defs')
+    var defs = svg.append('defs');
     defs.append('pattern')
         .attr({
           'id': 'antisense',
@@ -95,7 +97,6 @@ var NonEmptyGeneTrack = React.createClass({
   },
   updateVisualization: function() {
     var div = this.getDOMNode(),
-        range = this.props.range,
         width = div.offsetWidth,
         height = div.offsetHeight,
         svg = d3.select(div).select('svg');
@@ -127,7 +128,7 @@ var NonEmptyGeneTrack = React.createClass({
                     .map(x => [x, g.position.start()]))
       .enter()
       .append('rect')
-        .attr('class', 'exon')
+        .attr('class', 'exon');
 
     // The gene name goes in the center of the gene, modulo boundary effects.
     var textCenterX = g => {
@@ -182,7 +183,7 @@ var NonEmptyGeneTrack = React.createClass({
 
 var EmptyTrack = React.createClass({
   render: function() {
-    return <div className="genes empty">Zoom in to see genes</div>
+    return <div className="genes empty">Zoom in to see genes</div>;
   }
 });
 

src/GenomeTrack.js

@@ -2,6 +2,7 @@
  * A track which displays a reference genome.
  * @flow
  */
+'use strict';
 
 var React = require('react/addons'),
     _ = require('underscore'),
@@ -160,7 +161,7 @@ var NonEmptyGenomeTrack = React.createClass({
 
 var EmptyTrack = React.createClass({
   render: function() {
-    return <div className="reference empty">Zoom in to see bases</div>
+    return <div className="reference empty">Zoom in to see bases</div>;
   }
 });
 

src/RemoteFile.js

@@ -1,8 +1,10 @@
-/** @flow */
+
 /**
  * RemoteFile is a representation of a file on a remote server which can be
  * fetched in chunks, e.g. using a Range request.
+ * @flow
  */
+'use strict';
 
 var Q = require('q');
 

src/Root.js

@@ -2,15 +2,13 @@
  * Root of the React component tree.
  * @flow
  */
+'use strict';
 
 var React = require('react'),
     ContigInterval = require('./ContigInterval'),
     Controls = require('./Controls'),
     GenomeTrack = require('./GenomeTrack'),
-    GeneTrack = require('./GeneTrack'),
-    // TODO: make this an "import type" when react-tools 0.13.0 is out.
-    TwoBitDataSource = require('./TwoBitDataSource'),
-    types = require('./types');
+    GeneTrack = require('./GeneTrack');
 
 
 var Root = React.createClass({
@@ -24,15 +22,15 @@ var Root = React.createClass({
       range: (null: ?GenomeRange),
       basePairs: (null: any),
       genes: ([]: Array<any>)  // TODO import Gene type
-    }
+    };
   },
   componentDidMount: function() {
     // Note: flow is unable to infer this type through `this.propTypes`.
     var source = this.props.referenceSource;
     source.needContigs();
 
     source.on('contigs', () => { this.update() })
-          .on('newdata', () => { this.update() })
+          .on('newdata', () => { this.update() });
 
     source.on('contigs', () => {
       // this is here to facilitate faster iteration
@@ -44,7 +42,7 @@ var Root = React.createClass({
     });
 
     var geneSource = this.props.geneSource;
-    source.on('newdata', () => { this.update() });
+    geneSource.on('newdata', () => { this.update() });
 
     this.update();
   },

src/TwoBit.js

@@ -170,7 +170,7 @@ class TwoBit {
     return this.header.then(header => {
       var maybeSeq = _.findWhere(header.sequences, {name: contig}) ||
                      _.findWhere(header.sequences, {name: 'chr' + contig});
-      if (maybeSeq == null) {
+      if (maybeSeq === null || maybeSeq === undefined) {
         throw 'Invalid contig: ' + contig;
       }
       var seq = maybeSeq;  // for flow, see facebook/flow#266

src/TwoBitDataSource.js

@@ -21,9 +21,9 @@ var Events = require('backbone').Events,
     Q = require('q'),
     _ = require('underscore');
 
-// TODO: make this an "import type" when react-tools 0.13.0 is out.
-var TwoBit = require('./TwoBit'),
-    ContigInterval = require('./ContigInterval');
+var ContigInterval = require('./ContigInterval');
+
+import type * as TwoBit from './TwoBit';
 
 
 // Requests for 2bit ranges are expanded to begin & end at multiples of this
@@ -50,7 +50,7 @@ type TwoBitSource = {
 function expandRange(range) {
   var roundDown = x => x - x % BASE_PAIRS_PER_FETCH;
   var newStart = Math.max(1, roundDown(range.start())),
-      newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1)
+      newStop = roundDown(range.stop() + BASE_PAIRS_PER_FETCH - 1);
 
   return new ContigInterval(range.contig, newStart, newStop);
 }

src/bedtools.js

@@ -1,4 +1,5 @@
 /* @flow */
+'use strict';
 
 var _ = require('underscore');
 var Interval = require('./Interval');

src/formats/bbi.js

@@ -5,8 +5,7 @@
 
 'use strict';
 
-var jBinary = require('jbinary'),
-    {typeAtOffset} = require('./helpers');
+var {typeAtOffset} = require('./helpers');
 
 var TYPE_SET = {
   'jBinary.littleEndian': true,

src/formats/helpers.js

@@ -1,14 +1,16 @@
 /**
  * Helpers for specifying file formats using jBinary.
  */
+'use strict';
+
 var jBinary = require('jbinary');
 
 // Read a jBinary type at an offset in the buffer specified by another field.
 function typeAtOffset(typeName, offsetFieldName) {
   return jBinary.Template({
       baseType: typeName,
       read: function(context) {
-        if (+context[offsetFieldName] == 0) {
+        if (+context[offsetFieldName] === 0) {
           return null;
         } else {
           return this.binary.read(this.baseType, +context[offsetFieldName]);

src/formats/twoBitTypes.js

@@ -5,8 +5,6 @@
 
 'use strict';
 
-var jBinary = require('jbinary');
-
 var TYPE_SET = {
   'jBinary.littleEndian': true,
 

src/main.js

@@ -1,22 +1,22 @@
 /* @flow */
+'use strict';
+
 var React = require('react'),
     TwoBit = require('./TwoBit'),
     BigBed = require('./BigBed'),
     Root = require('./Root'),
     createTwoBitDataSource = require('./TwoBitDataSource'),
     createBigBedDataSource = require('./BigBedDataSource');
 
-var startMs = Date.now();
-// var genome = new TwoBit('http://www.biodalliance.org/datasets/hg19.2bit');
 var genome = new TwoBit('/hg19.2bit');
 var dataSource = createTwoBitDataSource(genome);
 
 var ensembl = new BigBed('/ensGene.bb');
 var ensemblDataSource = createBigBedDataSource(ensembl);
 
-var root = React.render(<Root referenceSource={dataSource}
-                              geneSource={ensemblDataSource} />,
-                        document.getElementById('root'));
+React.render(<Root referenceSource={dataSource}
+                   geneSource={ensemblDataSource} />,
+             document.getElementById('root'));
 
 window.ensembl = ensembl;
 window.genome = genome;

src/types.js

@@ -2,6 +2,8 @@
  * Common types used in many React components.
  * @flow
  */
+'use strict';
+
 var React = require('react');
 
 module.exports = {

src/utils.js

@@ -2,7 +2,7 @@
  * Grab-bag of utility functions.
  * @flow
  */
-
+'use strict';
 
 // Compare two tuples of equal length. Is t1 <= t2?
 // TODO: make this tupleLessOrEqual<T> -- it works with strings or booleans, too.

test/.jshintrc

@@ -0,0 +1,5 @@
+{
+  "extends": "../.jshintrc",
+
+  "expr": true  // chai assertions look like expressions to jshint
+}

test/BigBed-test.js

@@ -1,6 +1,6 @@
+'use strict';
 var chai = require('chai');
 var expect = chai.expect;
-var assert = chai.assert;
 
 var Q = require('q');
 var BigBed = require('../src/BigBed');
@@ -31,13 +31,13 @@ describe('BigBed', function() {
           expect(features[1].stop).to.equal(151079365);
 
           var rest0 = features[0].rest.split('\t');
-          expect(rest0).to.have.length(6)
+          expect(rest0).to.have.length(6);
           expect(rest0[0]).to.equal('MID_BLUE');
           expect(rest0[2]).to.equal('-');
           expect(rest0[5]).to.equal('0,0,128');
 
           var rest1 = features[1].rest.split('\t');
-          expect(rest1).to.have.length(6)
+          expect(rest1).to.have.length(6);
           expect(rest1[0]).to.equal('VIOLET_RED1');
           expect(rest1[2]).to.equal('-');
           expect(rest1[5]).to.equal('255,62,150');
@@ -50,8 +50,7 @@ describe('BigBed', function() {
     // The matches looks like this:
     // chrX 151071196 151072363 RED
     // chrX 151094536 151095703 PeachPuff
-    var red = [151071196, 151072362],  // note: stop is inclusive
-        peachpuff = [151094536, 151095702];
+    var red = [151071196, 151072362];  // note: stop is inclusive
 
     var bb = getTestBigBed();
     var expectN = n => features => {