From 166185e2c178608d824a6aeea088dc3bcaf4253f Mon Sep 17 00:00:00 2001
From: Alyssa Morrow <akmorrow@berkeley.edu>
Date: Wed, 27 Sep 2017 15:23:41 -0700
Subject: [PATCH] Fix for VariantTrack failing to parse strings as ints

3 flow fix
---
 src/main/data/feature.js                      |  8 ++---
 src/main/data/variant.js                      |  4 +--
 src/main/json/GA4GHVariantJson.js             |  2 +-
 src/test/data/feature-test.js                 | 32 +++++++++++++++++++
 src/test/data/variant-test.js                 | 31 ++++++++++++++++++
 src/test/viz/FeatureTrack-test.js             |  2 +-
 .../{VariantTrack.js => VariantTrack-test.js} |  0
 7 files changed, 71 insertions(+), 8 deletions(-)
 create mode 100644 src/test/data/feature-test.js
 create mode 100644 src/test/data/variant-test.js
 rename src/test/viz/{VariantTrack.js => VariantTrack-test.js} (100%)

diff --git a/src/main/data/feature.js b/src/main/data/feature.js
index 55f90605..04b72bea 100644
--- a/src/main/data/feature.js
+++ b/src/main/data/feature.js
@@ -18,8 +18,8 @@ class Feature {
    this.id = feature.id;
    this.featureType = feature.featureType;
    this.contig = feature.contig;
-   this.start = feature.start;
-   this.stop = feature.stop;
+   this.start = parseInt(feature.start);
+   this.stop = parseInt(feature.stop);
    this.score = feature.score;
   }
 
@@ -29,8 +29,8 @@ class Feature {
       id: ga4ghFeature.id,
       featureType: ga4ghFeature.featureType,
       contig: ga4ghFeature.referenceName,
-      start: ga4ghFeature.start,
-      stop: ga4ghFeature.end,
+      start: parseInt(ga4ghFeature.start),
+      stop: parseInt(ga4ghFeature.end),
       score: 1000
     });
   }
diff --git a/src/main/data/variant.js b/src/main/data/variant.js
index f0a47c88..c8177af6 100644
--- a/src/main/data/variant.js
+++ b/src/main/data/variant.js
@@ -23,7 +23,7 @@ class Variant {
 
   constructor(variant: Object) {
    this.contig = variant.contig;
-   this.position = variant.position;
+   this.position = parseInt(variant.position);
    this.ref = variant.ref;
    this.alt = variant.alt;
    this.id = variant.id;
@@ -36,7 +36,7 @@ class Variant {
    return new Variant(
     {
      contig: ga4ghVariant.referenceName,
-     position: ga4ghVariant.start,
+     position: parseInt(ga4ghVariant.start),
      id: ga4ghVariant.id,
      ref: ga4ghVariant.referenceBases,
      alt: ga4ghVariant.alternateBases,
diff --git a/src/main/json/GA4GHVariantJson.js b/src/main/json/GA4GHVariantJson.js
index 400485ea..b93519f6 100644
--- a/src/main/json/GA4GHVariantJson.js
+++ b/src/main/json/GA4GHVariantJson.js
@@ -21,7 +21,7 @@ function create(json: string): VcfDataSource {
 
   // fill variants with json
   if (!_.isEmpty(parsedJson)) {
-      variants = _.values(parsedJson.variants).map(feature => Variant.fromGA4GH(feature));
+      variants = _.values(parsedJson.variants).map(variant => Variant.fromGA4GH(variant));
   }
 
   function rangeChanged(newRange: GenomeRange) {
diff --git a/src/test/data/feature-test.js b/src/test/data/feature-test.js
new file mode 100644
index 00000000..f1e9295e
--- /dev/null
+++ b/src/test/data/feature-test.js
@@ -0,0 +1,32 @@
+/* @flow */
+'use strict';
+
+import {expect} from 'chai';
+import Feature from '../../main/data/feature';
+import _ from 'underscore';
+import RemoteFile from '../../main/RemoteFile';
+
+describe('Feature', function() {
+  var json;
+
+  before(function () {
+    return new RemoteFile('/test-data/features.ga4gh.chr1.120000-125000.json').getAllString().then(data => {
+      json = data;
+    });
+  });
+
+  it('should parse features from GA4GH', function(done) {
+
+      // parse json
+      var parsedJson = JSON.parse(json);
+      var features = _.values(parsedJson.features).map(feature => Feature.fromGA4GH(feature));
+
+      expect(features).to.have.length(9);
+      expect(features[0].contig).to.equal("chr1");
+      expect(features[0].start).to.equal(89295);
+      expect(features[0].stop).to.equal(120932);
+      expect(features[0].id).to.equal("WyIxa2dlbm9tZXMiLCJnZW5jb2RlX3YyNGxpZnQzNyIsIjE0MDUwOTE3MjM1NDE5MiJd");
+      expect(features[0].score).to.equal(1000);
+      done();
+  });
+});
diff --git a/src/test/data/variant-test.js b/src/test/data/variant-test.js
new file mode 100644
index 00000000..a09c302f
--- /dev/null
+++ b/src/test/data/variant-test.js
@@ -0,0 +1,31 @@
+/* @flow */
+'use strict';
+
+import {expect} from 'chai';
+import {Variant} from '../../main/data/variant';
+import _ from 'underscore';
+import RemoteFile from '../../main/RemoteFile';
+
+describe('Variant', function() {
+  var json;
+
+  before(function () {
+    return new RemoteFile('/test-data/variants.ga4gh.chr1.10000-11000.json').getAllString().then(data => {
+      json = data;
+    });
+  });
+
+  it('should parse variants from GA4GH', function(done) {
+
+      // parse json
+      var parsedJson = JSON.parse(json);
+      var variants = _.values(parsedJson.variants).map(variant => Variant.fromGA4GH(variant));
+
+      expect(variants).to.have.length(11);
+      expect(variants[0].contig).to.equal("1");
+      expect(variants[0].position).to.equal(10176);
+      expect(variants[0].ref).to.equal("A");
+      expect(variants[0].alt[0]).to.equal("AC");
+      done();
+  });
+});
diff --git a/src/test/viz/FeatureTrack-test.js b/src/test/viz/FeatureTrack-test.js
index c510b2db..319fc2b5 100644
--- a/src/test/viz/FeatureTrack-test.js
+++ b/src/test/viz/FeatureTrack-test.js
@@ -72,7 +72,7 @@ describe('FeatureTrack', function() {
 
         expect(features).to.have.length(4);
         expect(features.map(f => f.start)).to.deep.equal(
-            ["89295", "92230", "110953", "120725"]);
+            [89295, 92230, 110953, 120725]);
         p.destroy();
       });
   });
diff --git a/src/test/viz/VariantTrack.js b/src/test/viz/VariantTrack-test.js
similarity index 100%
rename from src/test/viz/VariantTrack.js
rename to src/test/viz/VariantTrack-test.js