Fix SNP clicking and Feature Details panel sections

Author: Sebastian Benjamin

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.tsx

@@ -1,4 +1,4 @@
-import { ConfigurationReference, getConf } from '@jbrowse/core/configuration';
+import { ConfigurationReference, getConf, readConfObject } from '@jbrowse/core/configuration';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { getContainingTrack, getContainingView, getSession } from '@jbrowse/core/util';
 import FilterListIcon from '@mui/icons-material/FilterList';
@@ -58,7 +58,7 @@ export default jbrowse => {
 
             // @ts-ignore
             const trackId = getConf(track, ['trackId'])
-            const detailsConfig = getConf(track, ['displays', '0', 'detailsConfig'])
+            const detailsConfig = readConfObject(self.configuration, 'detailsConfig')
 
             const widgetId = 'Variant-' + trackId;
             const featureWidget = session.addWidget(
@@ -78,7 +78,10 @@ export default jbrowse => {
       }))
 
       .views(self => {
-         const { renderProps: superRenderProps } = self
+         const {
+            renderProps: superRenderProps,
+            renderingProps: superRenderingProps,
+         } = self
          const filterMenu = {
             label: 'Filter By Attributes',
             icon: FilterListIcon,
@@ -140,6 +143,28 @@ export default jbrowse => {
                }
             },
 
+            renderingProps() {
+               const superProps = superRenderingProps()
+               return {
+                  ...superProps,
+                  async onFeatureClick(_, featureId) {
+                     const session = getSession(self)
+                     try {
+                        const f = featureId || self.featureIdUnderMouse
+                        if (!f) {
+                           self.clearFeatureSelection()
+                        }
+                        else {
+                           await self.selectFeatureById(f)
+                        }
+                     } catch (e) {
+                        console.error(e)
+                        session.notifyError(`${e}`, e)
+                     }
+                  },
+               }
+            },
+
             activeFilters() {
                const staticJexlFilters = (getConf(self, 'jexlFilters') || []).map((f: string) =>
                   f?.startsWith('jexl:') ? f : `jexl:${f}`,

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

@@ -105,8 +105,10 @@ export default jbrowse => {
         for (let display of displays){
             const tempProp = []
             for (let propertyName of display.properties){
-                // This value is not in the header, and is probably injected programmatically, so skip:
-                if (!featureInfoFields[propertyName]) {
+                // This value is not in the header, and is probably injected programmatically, so skip.
+                // Only apply this guard when featureInfoFields is actually populated (non-empty);
+                // when metadata is unavailable we still want to render configured sections.
+                if (Object.keys(featureInfoFields).length > 0 && !featureInfoFields[propertyName]) {
                     continue
                 }
 
@@ -377,7 +379,7 @@ export default jbrowse => {
             delete feat["INFO"]["ANN"]
         }
 
-        const sections = detailsConfig.sections || inferSections(feat, infoFields)
+        const sections = detailsConfig.sections?.length > 0 ? detailsConfig.sections : inferSections(feat, infoFields)
         const displays = makeDisplays(feat, sections, featureInfoFields, infoFields)
 
         // If a given INFO field is used in a specific section, dont include in the catch-all INFO section:

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

@@ -6,7 +6,6 @@ import ExtendedVariantDisplay from './ExtendedVariantDisplay';
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 
-import CanvasFeatureRenderer from "@jbrowse/plugin-canvas";
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import { configSchema as EVAdapterConfigSchema, EVAdapterClass } from './ExtendedVariantAdapter';
 

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -552,6 +552,11 @@ private JSONObject getVcfTrack(Logger log, ExpData targetFile, ReferenceGenome r
                 put("maxFeatureScreenDensity", 100);
                 put("mouseover", "jexl:'Position: ' + formatWithCommas(get(feature,'POS'))");
 
+                if (shouldHaveFreeTextSearch())
+                {
+                    put("supportsLuceneIndex", true);
+                }
+
                 JSONObject json = getExtraTrackConfig();
                 if (json != null && json.has("additionalFeatureMsg"))
                 {