Bugfix to JBrowse VariantTable sample filtering

Author: bbimber

jbrowse/src/client/JBrowse/utils.ts

@@ -33,7 +33,8 @@ export function passesSampleFilters(feature, sampleIDs){
 
     const featureVariant = feature.variant ?? feature.data
 
-    if (!featureVariant.SAMPLES || isEmptyObject(featureVariant.SAMPLES)) {
+    const samples = featureVariant.SAMPLES || featureVariant.samples
+    if (!samples || isEmptyObject(samples)) {
         return false
     }
 
@@ -49,8 +50,8 @@ export function passesSampleFilters(feature, sampleIDs){
     }
 
     for (const sampleId of sampleIDs) {
-        if (featureVariant.SAMPLES[sampleId]) {
-            const gt = featureVariant.SAMPLES[sampleId]["GT"][0]
+        if (samples[sampleId]) {
+            const gt = samples[sampleId]["GT"][0]
 
             // If any sample in the whitelist is non-WT, show this site. Otherwise filter.
             if (isVariant(gt)) {
@@ -100,7 +101,7 @@ export async function fetchSession(queryParam, sessionId, nativePlugins, refThem
             delete jsonRes.themeLightColor
             delete jsonRes.themeDarkColor
 
-            if(setBgColor) {
+            if (setBgColor) {
                 setBgColor(themeSecondaryColor)
             }
 
@@ -214,15 +215,23 @@ export function navigateToBrowser(sessionId, locString, trackId?: string, track?
 }
 
 function serializeSampleFilters(track) {
-    if(!track) {
+    if (!track) {
+        return undefined
+    }
+
+    if (!track.configuration.displays[0].renderer.activeSamples.value) {
         return undefined
     }
 
     return track.configuration.trackId + ":" + track.configuration.displays[0].renderer.activeSamples.value
 }
 
 function serializeInfoFilters(track) {
-    if(!track) {
+    if (!track) {
+        return undefined
+    }
+
+    if (!track.configuration.displays[0].renderer.infoFilters.valueJSON || isEmptyObject(track.configuration.displays[0].renderer.infoFilters.valueJSON)) {
         return undefined
     }
 
@@ -232,8 +241,8 @@ function serializeInfoFilters(track) {
 function handleFailure(error, sessionId?, trackId?, isTable?) {
     alert(error)
 
-    if(sessionId && trackId) {
-        if(isTable) {
+    if (sessionId && trackId) {
+        if (isTable) {
             navigateToTable(sessionId, "", trackId)
         } else {
             navigateToBrowser(sessionId, "", trackId)