Debug JBrowseTest failure on SqlServer agents (#133)

* Debug JBrowseTest failure on SqlServer agents
* Add jQuery and use isEmptyObject instead of Object.keys()
* Add raw images to VCS

Author: bbimber

jbrowse/package-lock.json

@@ -24,6 +24,7 @@
     "mobx-react": "^6.0.0",
     "mobx-state-tree": "3.14.1",
     "node-polyfill-webpack-plugin": "1.1.0",
+    "jquery": "^3.6.0",
     "path-browserify": "^1.0.1",
     "pkg": "^5.3.2",
     "react-google-charts": "^3.0.15",

jbrowse/package.json

@@ -12,6 +12,7 @@ import SvgOverlay from '@jbrowse/plugin-svg/src/SvgFeatureRenderer/components/Sv
 import {chooseGlyphComponent, layOut} from './util' // NEW: chooseGlyphComponent() in util updated to render SNVs as a diamond
 import {deserializeFilters} from '../../InfoFilterWidget/filterUtil' // NOTE: Now dependent on FilterWidget plugin
 import jexl from 'jexl'
+import { isEmptyObject } from 'jquery';
 
 const renderingStyle = {
     position: 'relative',
@@ -157,7 +158,7 @@ function passesSampleFilters(feature, sampleIDs){
         return true
     }
 
-    if (!feature.variant.SAMPLES || Object.keys(feature.variant.SAMPLES).length === 0) {
+    if (!feature.variant.SAMPLES || isEmptyObject(feature.variant.SAMPLES)) {
         return false
     }
 

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantRenderer/components/SvgFeatureRendering.js

@@ -319,20 +319,17 @@ private void testInferredDetails()
 
     private void testSampleFiltersFromUrl()
     {
-        beginAt("/home/jbrowse-jbrowse.view?session=mgap&sampleFilters=mgap:m00010");
+        // Note: this can be taxing on the browser, so load a more targeted region
+        beginAt("/home/jbrowse-jbrowse.view?session=mgap&sampleFilters=mgap:m00010&location=1:116,980,271..116,983,486");
         checker().takeScreenShot("Jbrowse1_OnLoad");
 
         waitForJBrowseToLoad();
         checker().takeScreenShot("Jbrowse2_OnLoad");
 
-        // NOTE: this should be replaced with something more specific
-        sleep(5000);
-        checker().takeScreenShot("Jbrowse3_OnLoad");
-
         // Wait for variants to load:
         getDriver().findElements(getVariantWithinTrack("mgap_hg38", "SNV A -> G"));
 
-        Assert.assertEquals("Incorrect number of variants", 18, getTotalVariantFeatures());
+        Assert.assertEquals("Incorrect number of variants", 3, getTotalVariantFeatures());
 
         openTrackMenuItem("Filter By Sample");
         waitForElement(Locator.tagWithText("h6", "Filter By Sample"));