Merge b7d0d24 into 70e49fb

lib/mocha.js

@@ -1,2 +1,3 @@
 declare function describe(description: string, spec: () => void): void;
 declare function it(expectation: string, assertion: (done: () => void) => void): void;
+declare function afterEach(fn: () => void): void;

src/Root.js

@@ -14,7 +14,8 @@ var React = require('react'),
 var Root = React.createClass({
   propTypes: {
     referenceSource: React.PropTypes.object.isRequired,
-    geneSource: React.PropTypes.object.isRequired
+    geneSource: React.PropTypes.object.isRequired,
+    initialRange: React.PropTypes.object.isRequired
   },
   getInitialState: function() {
     return {
@@ -34,11 +35,7 @@ var Root = React.createClass({
 
     source.on('contigs', () => {
       // this is here to facilitate faster iteration
-      this.handleRangeChange({
-        contig: 'chr17',
-        start: 7512444,
-        stop: 7512484
-      });
+      this.handleRangeChange(this.props.initialRange);
     });
 
     var geneSource = this.props.geneSource;

src/main.js

@@ -15,7 +15,8 @@ var ensembl = new BigBed('/ensGene.bb');
 var ensemblDataSource = createBigBedDataSource(ensembl);
 
 React.render(<Root referenceSource={dataSource}
-                   geneSource={ensemblDataSource} />,
+                   geneSource={ensemblDataSource}
+                   initialRange={{contig: "chr17", start: 7512444, stop: 7512484}} />,
              document.getElementById('root'));
 
 window.ensembl = ensembl;

test/BigBed-test.js

@@ -10,10 +10,7 @@ var ContigInterval = require('../src/ContigInterval');
 
 describe('BigBed', function() {
   function getTestBigBed() {
-    // This file was generated using UCSC tools:
-    // cd kent/src/utils/bedToBigBed/tests; make
-    // It is compressed, little endian, has autoSQL and two blocks.
-    return new BigBed('/test/data/itemRgb.bb');
+    return new BigBed('/test/data/itemRgb.bb');   // See test/data/README.md
   }
 
   it('should extract features in a range', function(done) {

test/BigBedDataSource-test.js

@@ -10,11 +10,7 @@ var BigBed = require('../src/BigBed'),
 
 describe('BigBedDataSource', function() {
   function getTestSource() {
-    // This file was created from Biodalliance's ensGene.bb via:
-    // bigBedToBed ensGene.bb ensGene.bed
-    // grep '^chr17   ' ensGene.bed > /tmp/ensGene17.bed
-    // bedToBigBed -type=bed12+2 /tmp/ensGene17.bed <(echo "chr17 78774742")
-    //             test/data/ensembl.chr17.bb
+    // See test/data/README.md
     return createBigBedDataSource(new BigBed('/test/data/ensembl.chr17.bb'));
   }
 

test/TwoBit-test.js

@@ -9,11 +9,7 @@ var TwoBit = require('../src/TwoBit');
 
 describe('TwoBit', function() {
   function getTestTwoBit() {
-    // This file was generated using UCSC tools:
-    // twoBitToFa -seqList=./test/seqList.txt hg19.2bit /tmp/extract.fa
-    // perl -i -pe 's/:.*//' /tmp/extract.fa
-    // faToTwoBit /tmp/extract.fa test/data/test.2bit
-    return new TwoBit('/test/data/test.2bit');
+    return new TwoBit('/test/data/test.2bit');   // See test/data/README.md
   }
 
   it('should have the right contigs', function(done) {

test/components-test.js

@@ -0,0 +1,89 @@
+/* @flow */
+'use strict';
+
+var chai = require('chai');
+var expect = chai.expect;
+
+var Q = require('q');
+
+var React = require('react/addons'),
+    TwoBit = require('../src/TwoBit'),
+    BigBed = require('../src/BigBed'),
+    Root = require('../src/Root'),
+    createTwoBitDataSource = require('../src/TwoBitDataSource'),
+    createBigBedDataSource = require('../src/BigBedDataSource');
+
+
+var WAIT_FOR_POLL_INTERVAL_MS = 100;
+function waitFor(predFn, timeoutMs) {
+  var def = Q.defer();
+
+  var checkTimeoutId = null;
+
+  var timeoutId = window.setTimeout(() => {
+    if (checkTimeoutId) window.clearTimeout(checkTimeoutId);
+    def.reject('Timed out');
+  }, timeoutMs);
+
+  var check = function() {
+    if (def.promise.isRejected()) return;
+    if (predFn()) {
+      def.resolve(null);  // no arguments needed
+      window.clearTimeout(timeoutId);
+    } else {
+      checkTimeoutId = window.setTimeout(check, WAIT_FOR_POLL_INTERVAL_MS);
+    }
+  };
+  checkTimeoutId = window.setTimeout(check, 0);
+
+  return def.promise;
+}
+
+
+describe('Root component', function() {
+  var genome = new TwoBit('/test/data/test.2bit');
+  var dataSource = createTwoBitDataSource(genome);
+
+  // This file contains just the TP53 gene, shifted so that it starts at the
+  // beginning of chr17 (to match test.2bit). See test/data/README.md.
+  var ensembl = new BigBed('/test/data/tp53.shifted.bb');
+  var ensemblDataSource = createBigBedDataSource(ensembl);
+
+  var testDiv = document.getElementById('testdiv');
+
+  afterEach(function() {
+    testDiv.innerHTML = '';  // avoid pollution between tests.
+  });
+
+  it('should render reference genome and genes', function(done) {
+    this.timeout(5000);
+
+    var div = document.createElement('div');
+    div.setAttribute('style', 'width: 800px; height: 200px;');
+    testDiv.appendChild(div);
+
+    // TODO: changing to {start:1, stop:50} makes the test fail.
+    React.render(<Root referenceSource={dataSource}
+                       geneSource={ensemblDataSource}
+                       initialRange={{contig:"chr17", start: 100, stop: 150}} />, div);
+
+    var ready = (() => 
+      div.querySelectorAll('.basepair').length > 0 &&
+      div.querySelectorAll('.gene').length > 0
+    );
+
+    waitFor(ready, 5000)
+      .then(() => {
+        var basepairs = div.querySelectorAll('.basepair');
+        expect(basepairs).to.have.length.at.least(10);
+        var geneNames = div.querySelectorAll('.gene text');
+        expect(geneNames.length).to.equal(1);
+        expect(geneNames[0].textContent).to.equal('TP53');
+
+        // Note: there are 11 exons, but two are split into coding/non-coding
+        expect(div.querySelectorAll('.gene .exon').length).to.equal(13);
+        done();
+      })
+      .done();
+  });
+});

test/coverage.html

@@ -5,6 +5,7 @@
   <link rel="stylesheet" href="../node_modules/mocha/mocha.css" />
 </head>
 <body>
+  <div id="testdiv"></div>
   <div id="mocha"></div>
 
   <!-- Polyfills for PhantomJS -->
@@ -15,9 +16,6 @@
   <!-- Mocha -->
   <script src="../node_modules/mocha/mocha.js"></script>
   <script>mocha.setup('bdd')</script>
-
-  <!--<script src="../build/cov/tests-debug.js"></script>-->
-  <!--<script src="../build/tests-debug.js"></script>-->
   <script src="../build/cov/tests.js"></script>
 
   <script>

test/data/README.md

@@ -0,0 +1,49 @@
+This directory contains many small data files used in testing.
+
+This file documents how they were generated.
+
+
+#### test.2bit
+
+This is a small subset of the hg19 reference genome. It contains small swaths
+of chr1 and chr22 and a larger swath of chr17. It was generated from hg19.2bit
+using UCSC tools:
+
+    curl -O http://www.biodalliance.org/datasets/hg19.2bit
+    twoBitToFa -seqList=./test/data/seqList.txt hg19.2bit /tmp/extract.fa
+    perl -i -pe 's/:.*//' /tmp/extract.fa
+    faToTwoBit /tmp/extract.fa test/data/test.2bit
+
+
+#### itemRgb.bb, itemRgb.bed
+
+This file was generated from UCSC test data:
+
+    cd kent/src/utils/bedToBigBed/tests
+    make
+    cp output/itemRgb.bb $PILEUP/test/data/
+
+It is compressed, little endian, has autoSQL and two blocks.
+
+`itemRgb.bed` is copied unmodified from `bedToBigBed/tests/input`.
+
+
+#### ensembl.chr17.bb
+
+This file is derived from `ensGene.bb`. It contains just the genes on chr17.
+
+    curl -O http://www.biodalliance.org/datasets/ensGene.bb
+    bigBedToBed ensGene.bb ensGene.bed
+    grep '^chr17\t' ensGene.bed > /tmp/ensGene17.bed
+    bedToBigBed -type=bed12+2 /tmp/ensGene17.bed <(echo "chr17 78774742") test/data/ensembl.chr17.bb
+
+#### tp53.shifted.bb
+
+This is a subset of `ensembl.chr17.bb`, shifted to match the coordinates in
+`test.2bit`:
+
+    curl -O http://www.biodalliance.org/datasets/ensGene.bb
+    bigBedToBed ensGene.bb ensGene.bed
+    grep '^chr17\t' ensGene.bed | grep TP53 | perl -pe 's/(75\d{4,})/$1-7512444/ge' > /tmp/tp53.shifted.bed
+    bedToBigBed -type=bed12+2 /tmp/tp53.shifted.bed <(echo "chr17 78774742") test/data/tp53.shifted.bb
+

test/runner.html

@@ -5,6 +5,7 @@
   <link rel="stylesheet" href="../node_modules/mocha/mocha.css" />
 </head>
 <body>
+  <div id="testdiv"></div>
   <div id="mocha"></div>
 
   <!-- Polyfills for PhantomJS -->