Merge branch '1556-order-of-icons' into 'devel_16.0.x'

always show gentic data overlays

See merge request !1358

CHANGELOG

 minerva (16.0.0~beta.3) stable; urgency=medium
+  * Bug fix: show genetic data overlays in InfoWindow even when no data is
+    available (#1562)
   * Bug fix: speed of opening map is improved (#1558)
   * Bug fix: typo (#1555)
   * Bug fix: gene mapping with empty url caused issues when opening info window
@@ -8,7 +10,7 @@ minerva (16.0.0~beta.3) stable; urgency=medium
   * Bug fix: sometimes wrong icn numbers were attached to search results
     (#1556)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Sep 2021 08:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 27 Sep 2021 14:00:00 +0200
 
 minerva (16.0.0~beta.2) stable; urgency=medium
   * Small improvement: backgrounds are separated from general overlays (#1532)

frontend-js/src/main/js/map/window/AliasInfoWindow.js

@@ -366,6 +366,12 @@ AliasInfoWindow.prototype.adjustPileupRangeVisibility = function (pileupRange) {
     pileupRange.stop += Math.ceil((50 - dist) / 2);
   }
 
+  if (pileupRange.stop < pileupRange.start) {
+    var tmp = pileupRange.stop;
+    pileupRange.stop = pileupRange.start;
+    pileupRange.start = tmp;
+  }
+
   if (pileupRange.start < 0) {
     pileupRange.stop -= pileupRange.start;
     pileupRange.start = 0;
@@ -414,8 +420,12 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
   var promises = [];
   var overlaysData = [];
 
-  overlays.forEach(function (overlay) {
+  var overlayGeneticInformation = [];
+
+  overlays.forEach(function (overlay, index) {
     promises.push(overlay.getFullAliasesById(self.getAlias().getId()));
+    globalGeneVariants[index] = [];
+    overlayGeneticInformation[index] = (overlay.getType() === LayoutAlias.GENETIC_VARIANT);
     if (overlay.getType() === LayoutAlias.GENETIC_VARIANT) {
       geneticInformation = true;
       promises.push(self.getCustomMap().getTopMap().getReferenceGenome(overlay.getGenomeType(),
@@ -429,7 +439,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
           logger.warn("Genome for " + overlay.getGenomeType() + ","
             + overlay.getGenomeVersion() + " not loaded");
         }
-      }, function () {
+      }).catch(function () {
         logger.warn("Genome for " + overlay.getGenomeType() + ","
           + overlay.getGenomeVersion() + " not loaded");
 
@@ -472,7 +482,6 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
     }
     for (i = 0; i < overlaysData.length; i++) {
       var data = overlaysData[i];
-      globalGeneVariants[i] = [];
       if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
         var geneVariants = data.getGeneVariants();
         for (var j = 0; j < geneVariants.length; j++) {
@@ -495,9 +504,12 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
           contentElement.innerHTML = "No reference genome defined for this MINERVA instance, cannot display variant data.";
         }
       } else {
-        for (i = 0; i < overlaysData.length; i++) {
-          if (globalGeneVariants[i].length > 0) {
-            var vcfContent = self.createVcfString(globalGeneVariants[i]);
+        for (i = 0; i < overlays.length; i++) {
+          var vcfContent = undefined;
+          if (overlayGeneticInformation[i]) {
+            vcfContent = self.createVcfString(globalGeneVariants[i]);
+          }
+          if (vcfContent !== undefined) {
             pileupSource.push({
               viz: pileup.viz.variants(),
               data: pileup.formats.vcf({