flow passes

.flowconfig

@@ -14,6 +14,7 @@
 .*node_modules/jshint.*
 .*node_modules/jstransformify.*
 .*node_modules/uglify.*
+.*node_modules/module-deps.*
 .*node_modules/data-canvas.*
 .*node_modules/babel.*
 .*node_modules/d3.*
@@ -31,3 +32,6 @@
 [libs]
 lib
 node_modules/data-canvas/flowtype
+
+[options]
+suppress_comment= \\(.\\|\n\\)*\\$FlowIgnore

package.json

@@ -87,7 +87,7 @@
     "eslint-plugin-promise": "^4.0.0",
     "eslint-plugin-react": "7.22.0",
     "exorcist": "^0.4.0",
-    "flow-bin": "^0.144.0",
+    "flow-bin": "^0.120.1",
     "http-server": "^0.12.3",
     "install": "^0.13.0",
     "istanbul": "^0.4.5",

src/main/VisualizationWrapper.js

@@ -85,7 +85,7 @@ class VisualizationWrapper extends React.Component<Props, State> {
     window.removeEventListener('resize', this.onResizeListener);
   }
 
-  getScale(): (num: number)=>number {
+  getScale(): any {
     if (!this.props.range) return x => x;
     return d3utils.getTrackScale(this.props.range, this.state.width);
   }

src/main/data/BigBed.js

@@ -162,7 +162,7 @@ class ImmediateBigBed {
   contigMap: {[key:string]: number};
   chrIdToContig: string[];
 
-  constructor(remoteFile, header, cirTree, contigMap: {[key:string]: number}) {
+  constructor(remoteFile: RemoteFile, header: Object, cirTree: Object, contigMap: {[key:string]: number}) {
     this.remoteFile = remoteFile;
     this.header = header;
     this.cirTree = cirTree;

src/main/data/formats/bamTypes.js

@@ -56,6 +56,7 @@ var ThickAlignment = _.extend(_.clone(ThinAlignment), {
   auxiliary: ['array', {
     tag: ['string', 2],
     val_type: 'char',
+    // $FlowIgnore: TODO remove flow suppression
     value: ['if', ctx => ctx.val_type == 'B', {
              val_type: 'char',
              num_values: 'int32',

src/main/data/gene.js

@@ -75,7 +75,7 @@ class Gene {
       codingRegion = new Interval(parseInt(thickStart.values[0].stringValue),
           parseInt(thickEnd.values[0].stringValue));
     } else {
-      codingRegion = new Interval(position.start(), position.end());
+      codingRegion = new Interval(position.start(), position.stop());
     }
 
     return new Gene({

src/main/viz/CoverageTrack.js

@@ -9,7 +9,6 @@ import type {DataSource} from '../sources/DataSource';
 import Feature from '../data/feature';
 import type {DataCanvasRenderingContext2D} from 'data-canvas';
 import type {BinSummary} from './CoverageCache';
-import type {Scale} from './d3utils';
 import type {State} from '../types';
 import type {VizProps} from '../VisualizationWrapper';
 
@@ -199,7 +198,7 @@ class CoverageTrack extends React.Component<VizProps<DataSource<Alignment | Feat
     return <canvas ref='canvas' onClick={this.handleClick.bind(this)} />;
   }
 
-  getScale(): Scale {
+  getScale(): any {
     return d3utils.getTrackScale(this.props.range, this.props.width);
   }
 
@@ -248,7 +247,7 @@ class CoverageTrack extends React.Component<VizProps<DataSource<Alignment | Feat
   }
 
   // Draw three ticks on the left to set the scale for the user
-  renderTicks(ctx: DataCanvasRenderingContext2D, yScale: (num: number)=>number) {
+  renderTicks(ctx: DataCanvasRenderingContext2D, yScale: any) {
     var axisMax = yScale.domain()[0];
     [0, Math.round(axisMax / 2), axisMax].forEach(tick => {
       // Draw a line indicating the tick

src/main/viz/GeneTrack.js

@@ -8,7 +8,6 @@ import type {Strand} from '../Alignment';
 import Gene from '../data/gene';
 import type {DataSource} from '../sources/DataSource';
 import type {VizProps} from '../VisualizationWrapper';
-import type {Scale} from './d3utils';
 import type {State} from '../types';
 
 import GenericFeature from '../data/genericFeature';
@@ -113,7 +112,7 @@ class GeneTrack extends React.Component<VizProps<DataSource<Gene>>, State> {
     this.updateVisualization();
   }
 
-  getScale(): Scale {
+  getScale(): any {
     return d3utils.getTrackScale(this.props.range, this.props.width);
   }
 

src/main/viz/GenotypeTrack.js

@@ -8,7 +8,6 @@ import type {VcfDataSource} from '../sources/VcfDataSource';
 import type {VariantContext} from '../data/variant';
 import type {DataCanvasRenderingContext2D} from 'data-canvas';
 import type {VizProps} from '../VisualizationWrapper';
-import type {Scale} from './d3utils';
 
 import React from 'react';
 import _ from 'underscore';
@@ -184,7 +183,7 @@ class GenotypeTrack extends React.Component<VizProps<VcfDataSource>, State> {
         this.updateVisualization();
   }
 
-  getScale(): Scale {
+  getScale(): any {
     return d3utils.getTrackScale(this.props.range, this.props.width - LABEL_WIDTH);
   }
 

src/main/viz/PileupTrack.js

@@ -11,7 +11,6 @@ import type {VisualAlignment, InsertStats} from './PileupCache';
 import type {VisualGroup} from './AbstractCache';
 import type {DataCanvasRenderingContext2D} from 'data-canvas';
 import type {VizProps} from '../VisualizationWrapper';
-import type {Scale} from './d3utils';
 import type {State, NetworkStatus} from '../types';
 
 import React from 'react';
@@ -310,7 +309,7 @@ class PileupTrack extends React.Component<VizProps<DataSource<Alignment>>, State
     this.updateVisualization();
   }
 
-  getScale(): Scale {
+  getScale(): any {
     return d3utils.getTrackScale(this.props.range, this.props.width);
   }
 

src/test/MappedRemoteFile.js

@@ -61,7 +61,7 @@ class MappedRemoteFile extends RemoteFile {
         return buf;
       });
     } else {
-      return Q.reject(`Request for ${originalRequest} is not mapped in ${this.url}`);
+      return Q.reject(`Request for ${originalRequest.toString()} is not mapped in ${this.url}`);
     }
   }
 

src/test/components-test.js

@@ -83,8 +83,8 @@ describe('pileup', function() {
   };
 
   // TODO: consider moving this into the data-canvas library
-  function hasCanvasAndObjects(div, selector) {
-    return div.querySelector(selector + ' canvas') && drawnObjects(div, selector).length > 0;
+  function hasCanvasAndObjects(div, selector): boolean {
+    return div.querySelector(selector + ' canvas') !== null && drawnObjects(div, selector).length > 0;
   }
 
   var ready = ((): boolean =>

src/test/sources/CytoBandDataSource-test.js

@@ -30,7 +30,7 @@ describe('CytoBandDataSource', function() {
       expect(chr.bands[0].value).to.equal('gvar');
       done();
     });
-    source.rangeChanged(range);
+    source.rangeChanged({contig: range.contig, start: range.start(), stop: range.stop()});
   });
 
   it('should allow a mix of chr and non-chr', function(done) {