rm nested callbacks in GA4GHAlignment-test

hammerlab · Sep 7, 2017 · 74af57e · 74af57e
1 parent 074457c
commit 74af57e
Showing 1 changed file with 32 additions and 30 deletions.
diff --git a/src/test/GA4GHAlignment-test.js b/src/test/GA4GHAlignment-test.js
@@ -9,14 +9,10 @@ import Bam from '../main/data/bam';
 
 describe('GA4GHAlignment', function() {
   var sampleAlignments = [];
-  var matchingBamAlignments = [];
 
   before(function() {
     return new RemoteFile('/test-data/alignments.ga4gh.1.10000-11000.json').getAllString().then(data => {
       sampleAlignments = JSON.parse(data).alignments;
-      new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json').getAllString().then(bamData => {
-        matchingBamAlignments = JSON.parse(bamData).alignments;
-      });
     });
   });
 
@@ -43,35 +39,41 @@ describe('GA4GHAlignment', function() {
 
   it('should match SamRead', function() {
     var bam = new Bam(new RemoteFile('/test-data/chr17.1-250.bam'));
-    return bam.readAll().then(({alignments: samReads}) => {
-      // This is a workaround. See https://github.com/ga4gh/server/issues/488
-      samReads.splice(-1, 1);
+    var json = new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json');
 
-      expect(matchingBamAlignments.length).to.equal(samReads.length);
-      for (var i = 0; i < matchingBamAlignments.length; i++) {
-        var ga4gh = new GA4GHAlignment(matchingBamAlignments[i]),
-            bam = samReads[i];
-        expect(ga4gh.getSequence()).to.equal(bam.getSequence());
-        var interval = ga4gh.getInterval();
-        expect(interval.start()).to.equal(bam.pos);
+    json.getAllString().then(data => {
+      var matchingBamAlignments = JSON.parse(data).alignments;
 
-        // See https://github.com/ga4gh/server/issues/491
-        // expect(ga4gh.getStrand()).to.equal(bam.getStrand());
-        // For the if statement, see https://github.com/ga4gh/server/issues/492
-        var quality = ga4gh.getQualityScores();
-        if (quality.length) {
-          expect(quality).to.deep.equal(bam.getQualityScores());
-        }
-        expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps);
-        // After ga4gh#491, change this to a .deep.equal on getMateProperties()
-        var ga4ghMate = ga4gh.getMateProperties(),
-            bamMate = bam.getMateProperties();
-        expect(!!ga4ghMate).to.equal(!!bamMate);
-        if (ga4ghMate && bamMate) {
-          expect(ga4ghMate.ref).to.equal(bamMate.ref);
-          expect(ga4ghMate.pos).to.equal(bamMate.pos);
+      return bam.readAll().then(({alignments: samReads}) => {
+        // This is a workaround. See https://github.com/ga4gh/server/issues/488
+        samReads.splice(-1, 1);
+
+        expect(matchingBamAlignments.length).to.equal(samReads.length);
+        for (var i = 0; i < matchingBamAlignments.length; i++) {
+          var ga4gh = new GA4GHAlignment(matchingBamAlignments[i]),
+              bam = samReads[i];
+          expect(ga4gh.getSequence()).to.equal(bam.getSequence());
+          var interval = ga4gh.getInterval();
+          expect(interval.start()).to.equal(bam.pos);
+
+          // See https://github.com/ga4gh/server/issues/491
+          // expect(ga4gh.getStrand()).to.equal(bam.getStrand());
+          // For the if statement, see https://github.com/ga4gh/server/issues/492
+          var quality = ga4gh.getQualityScores();
+          if (quality.length) {
+            expect(quality).to.deep.equal(bam.getQualityScores());
+          }
+          expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps);
+          // After ga4gh#491, change this to a .deep.equal on getMateProperties()
+          var ga4ghMate = ga4gh.getMateProperties(),
+              bamMate = bam.getMateProperties();
+          expect(!!ga4ghMate).to.equal(!!bamMate);
+          if (ga4ghMate && bamMate) {
+            expect(ga4ghMate.ref).to.equal(bamMate.ref);
+            expect(ga4ghMate.pos).to.equal(bamMate.pos);
+          }
         }
-      }
+      });
     });
   });
 });