Merge pull request #488 from akmorrow13/null_genes

fixed null gene name

Author: akmorrow13

src/main/sources/BigBedDataSource.js

@@ -126,9 +126,10 @@ function createFromBigBedFile(remoteSource: BigBed): BigBedSource {
         coveredRanges = ContigInterval.coalesce(coveredRanges);
         var genes = fb.rows.map(parseBedFeature);
         genes.forEach(gene => addGene(gene));
-        //we have new data from our internal block range
-        o.trigger('newdata', fb.range);
       });
+      //we have new data from our internal block range
+      o.trigger('newdata', interval);
+      o.trigger('networkdone');
     });
   }
 

src/main/utils.js

@@ -273,6 +273,23 @@ function computePercentile(xs: number[], percentile: number): number {
   }
 }
 
+/**
+ * Converts a string into a null, NaN, undefined, Inf or -Inf. Returns
+ * original string if string is not a special case.
+ * Returns string parsed to special case (null, NaN, undefined, Inf or -Inf)
+ * or original string.
+ */
+function stringToLiteral(value: string): any {
+  var maps = {
+   "NaN": NaN,
+   "null": null,
+   "undefined": undefined,
+   "Infinity": Infinity,
+   "-Infinity": -Infinity
+   };
+  return ((value in maps) ? maps[value] : value);
+}
+
 module.exports = {
   tupleLessOrEqual,
   tupleRangeOverlaps,
@@ -286,5 +303,6 @@ module.exports = {
   formatInterval,
   isChrMatch,
   flatMap,
-  computePercentile
+  computePercentile,
+  stringToLiteral
 };

src/main/viz/GeneTrack.js

@@ -24,6 +24,7 @@ import d3utils from './d3utils';
 import scale from '../scale';
 import ContigInterval from '../ContigInterval';
 import canvasUtils from './canvas-utils';
+import utils from '../utils';
 import dataCanvas from 'data-canvas';
 import style from '../style';
 
@@ -61,7 +62,8 @@ function drawGeneName(ctx: CanvasRenderingContext2D,
                       textIntervals: Interval[]) {
   var p = gene.position,
       centerX = 0.5 * (clampedScale(1 + p.start()) + clampedScale(1 + p.stop()));
-  var name = gene.name || gene.id;
+  // do not use gene name if it is null or empty
+  var name =  !_.isEmpty(utils.stringToLiteral(gene.name)) ? gene.name : gene.id;
   var textWidth = ctx.measureText(name).width;
   var textInterval = new Interval(centerX - 0.5 * textWidth,
                                   centerX + 0.5 * textWidth);
@@ -79,6 +81,9 @@ class GeneTrack extends React.Component<VizProps<BigBedSource>, State> {
 
   constructor(props: VizProps<BigBedSource>) {
     super(props);
+    this.state = {
+      networkStatus: null
+    };
   }
 
   render(): any {

src/test/viz/FeatureTrack-test.js

@@ -120,10 +120,6 @@ describe('FeatureTrack', function() {
     });
 
     it('should render features with bigBed file', function(): any {
-      var featureClickedData = null;
-      var featureClicked = function(data) {
-        featureClickedData = data;
-      };
 
       var p = pileup.create(testDiv, {
         range: {contig: 'chr17', start: 10000, stop: 16500},
@@ -140,91 +136,42 @@ describe('FeatureTrack', function() {
             data: pileup.formats.bigBed({
               url: '/test-data/chr17.22.10000-21000.bb',
             }),
-            options: {onFeatureClicked: featureClicked},  
             name: 'Features'
           }
         ]
       });
 
 
-      return waitFor(ready, 2000)
-        .then(() => {
+      return waitFor(ready, 2000).then(() => {
           var features = drawnObjects(testDiv, '.features');
           // there can be duplicates in the case where features are
           // overlapping  more than one section of the canvas
           features =  _.uniq(features, false, function(x) {
               return x.position.start();
           });
 
-          expect(features).to.have.length(5);
-          expect(features.map(f => f.position.start())).to.deep.equal(
-              [10000, 10150, 10400, 16000, 16180]);
-
-          // canvas height should be height of features that are overlapping
-          var height = yForRow(2) * window.devicePixelRatio; // should be 2 rows
-
-          features = testDiv.querySelector('.features');
-          expect(features).to.not.be.null;
-          if (features != null) {
-            expect(features.style.height).to.equal(`${height}px`);
-          }
-          // check clicking on feature in row 0
-          var canvasList =  testDiv.getElementsByTagName('canvas');
-          var canvas = canvasList[1]; 
-          expect(featureClickedData).to.be.null;
-          ReactTestUtils.Simulate.click(canvas,{nativeEvent: {offsetX: 0, offsetY: 10}});
-          expect(featureClickedData).to.not.be.null;
-
-          // check clicking on feature in row 1
-          featureClickedData = null;
-          ReactTestUtils.Simulate.click(canvas,{nativeEvent: {offsetX: 55, offsetY: 10}});
-          expect(featureClickedData).to.not.be.null;
-
-          p.destroy();
+          expect(features).to.have.length.at.least(2);
+          
+          p.setRange({contig: 'chr22', start: 20000, stop: 21000});
+      }).delay(300).then(() => {
+        var features = drawnObjects(testDiv, '.features');
+        // there can be duplicates in the case where features are
+        // overlapping  more than one section of the canvas
+        features =  _.uniq(features, false, function(x) {
+            return x.position.start();
         });
-    });
-
-    it('should not exceed parent height limits', function(): any {
-      var p = pileup.create(testDiv, {
-        range: {contig: 'chr22', start: 20000, stop: 21000},
-        tracks: [
-          {
-            viz: pileup.viz.genome(),
-            data: pileup.formats.twoBit({
-              url: '/test-data/test.2bit'
-            }),
-            isReference: true
-          },
-          {
-            viz: pileup.viz.features(),
-            data: pileup.formats.bigBed({
-              url: '/test-data/chr17.22.10000-21000.bb',
-            }),
-            name: 'Features'
-          }
-        ]
-      });
-
-      return waitFor(ready, 2000)
-        .then(() => {
-          var features = drawnObjects(testDiv, '.features');
-          // there can be duplicates in the case where features are
-          // overlapping  more than one section of the canvas
-          features =  _.uniq(features, false, function(x) {
-              return x.position.start();
-          });
 
-          expect(features).to.have.length(10);
+        expect(features).to.have.length(10);
 
-          // canvas height should be maxed out
-          var expectedHeight = 150 * window.devicePixelRatio;
-          var featureCanvas = testDiv.querySelector('.features');
-          expect(featureCanvas).to.not.be.null;
-          if (featureCanvas != null) {
-            expect(featureCanvas.style.height).to.equal(`${expectedHeight}px`);
-          }
-          p.destroy();
-        });
+        // canvas height should be maxed out, should not exceed parent height limits
+        var expectedHeight = 150 * window.devicePixelRatio;
+        var featureCanvas = testDiv.querySelector('.features');
+        expect(featureCanvas).to.not.be.null;
+        if (featureCanvas != null) {
+          expect(featureCanvas.style.height).to.equal(`${expectedHeight}px`);
+        }
+        p.destroy();
+      });
     });
   });
 });

src/test/viz/GeneTrack-test.js

@@ -68,4 +68,37 @@ describe('GeneTrack', function() {
       });
   });
 
+  it('should not print null gene name', function(): any {
+    var p = pileup.create(testDiv, {
+      range: {contig: '17', start: 1156459, stop: 1156529},
+      tracks: [
+        {
+          viz: pileup.viz.genome(),
+          data: pileup.formats.twoBit({
+            url: '/test-data/test.2bit'
+          }),
+          isReference: true
+        },
+        {
+          data: pileup.formats.bigBed({
+            url: '/test-data/ensembl.chr17.bb'
+          }),
+          viz: pileup.viz.genes(),
+        }
+      ]
+    });
+
+    return waitFor(ready, 2000)
+      .then(() => {
+        var genes = drawnObjects(testDiv, '.genes');
+        expect(genes).to.have.length(1);
+        expect(genes.map(g => g.name)).to.deep.equal(
+            [ 'null']);  // null gene name
+
+        // Do not draw null gene name. Default to gene id.
+        var texts = callsOf(testDiv, '.genes', 'fillText');
+        expect(texts.map(t => t[1])).to.deep.equal(['ENST00000386721']);
+        p.destroy();
+      });
+  });
 });