Restore SNP labels

Author: Sebastian Benjamin

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.tsx

@@ -337,6 +337,9 @@ export default jbrowse => {
         const [infoFields, setInfoFields] = useState<Map<string, FieldModel>>(null)
 
         const feat = JSON.parse(JSON.stringify(feature))
+        feat["vcfMetadataInfo"] = Object.fromEntries(
+            Object.entries(featureInfoFields).map(([k, v]: [string, any]) => [k, v?.Description || v]),
+        )
         const { samples } = feat
         feat["samples"] = null
 

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts

@@ -1,5 +1,6 @@
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
+import { LinearBasicDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import ExtendedVariantWidget from './ExtendedVariantWidget';
 import ExtendedVariantDisplay from './ExtendedVariantDisplay';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
@@ -62,7 +63,6 @@ export default class ExtendedVariantPlugin extends Plugin {
         const WidgetType = jbrequire('@jbrowse/core/pluggableElementTypes/WidgetType')
         const TrackType = jbrequire('@jbrowse/core/pluggableElementTypes/TrackType')
         const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin',) as import('@jbrowse/plugin-linear-genome-view').default
-        const { BaseLinearDisplayComponent } = LGVPlugin.exports
 
         pluginManager.addAdapterType(() =>
             new AdapterType({
@@ -93,7 +93,9 @@ export default class ExtendedVariantPlugin extends Plugin {
                 stateModel,
                 trackType: 'ExtendedVariantTrack',
                 viewType: 'LinearGenomeView',
-                ReactComponent: BaseLinearDisplayComponent,
+                // Use LinearBasicDisplayComponent so canvas floating labels are rendered.
+                // BaseLinearDisplayComponent alone does not mount FloatingLabels.
+                ReactComponent: LinearBasicDisplayComponent,
             })
         })
 

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -715,10 +715,10 @@ else if (MGAP.equalsIgnoreCase(form.getSession()))
             else if (MGAP_FILTERED.equalsIgnoreCase(form.getSession()))
             {
                 resp = getDemoSession("external/mGAPSession.json");
-                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("activeSamples", "m00004,m00005");
-                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("palette", "AF");
-                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("supportsLuceneIndex", true);
-                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).getJSONObject("renderer").put("infoFilters", new JSONArray(){{
+                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("activeSamples", "m00004,m00005");
+                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("palette", "AF");
+                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("supportsLuceneIndex", true);
+                resp.getJSONArray("tracks").getJSONObject(0).getJSONArray("displays").getJSONObject(0).put("infoFilters", new JSONArray(){{
                     put("AF:gt:0.1");
                 }});
 

jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java

@@ -143,10 +143,19 @@ public static By getVariantWithinTrack(BaseWebDriverTest test, String trackId, S
     {
         Locator.XPathLocator l = getTrackLocator(test, trackId, true);
         test.waitForElementToDisappear(Locator.tagWithText("p", "Loading"));
-        l = l.append(Locator.xpath("//*[name()='text' and contains(text(), '" + variantText + "')]")).notHidden().parent();
-        if (appendPolygon){
-            l = l.append("/*[name()='polygon']");
+
+        String svgPath = "//*[name()='text' and contains(text(), '" + variantText + "')]";
+        if (appendPolygon)
+        {
+            svgPath += "/parent::*/*[name()='polygon']";
         }
+        else
+        {
+            svgPath += "/parent::*";
+        }
+
+        String canvasPath = "//div[@data-feature-id and contains(normalize-space(.), '" + variantText + "')]";
+        l = l.append(Locator.xpath("(" + svgPath + "|" + canvasPath + ")")).notHidden();
 
         test.waitForElement(l);