Fix JEXL instance for browser filtration

Author: Sebastian Benjamin

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/ExtendedVcfFeature.ts

@@ -8,6 +8,16 @@ export default class ExtendedVcfFeature extends VcfFeature {
         super(args)
     }
 
+    toJSON() {
+        const ret: any = super.toJSON()
+
+        // Preserve VCF INFO header metadata through JSON/snapshot flows used by
+        // JBrowse widgets. parser is not guaranteed to survive serialization.
+        ret.vcfMetadataInfo = (this as any).parser?.metadata?.INFO || {}
+
+        return ret
+    }
+
     static extractImpact(variant: Variant) {
         // Only append if not present:
         if (variant.INFO["IMPACT"]) {

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

@@ -135,6 +135,7 @@ export default jbrowse => {
                   rendererConfig: config,
                   filters: new SerializableFilterChain({
                      filters: this.activeFilters(),
+                     jexl: jbrowse.jexl,
                   }),
                }
             },

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

@@ -333,7 +333,7 @@ export default jbrowse => {
         const { model } = props
         const detailsConfig = JSON.parse(JSON.stringify(model.detailsConfig || {}))
         const feature = model.featureData
-        const featureInfoFields = feature.parser.metadata.INFO
+        const featureInfoFields = feature.vcfMetadataInfo || feature.parser?.metadata?.INFO || {}
         const [infoFields, setInfoFields] = useState<Map<string, FieldModel>>(null)
 
         const feat = JSON.parse(JSON.stringify(feature))

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

@@ -16,6 +16,7 @@ import SampleFilterWidget from './SampleFilterWidget';
 import GlyphType from '@jbrowse/core/pluggableElementTypes/GlyphType';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { emphasize } from '@jbrowse/core/util/color';
+import jexl from '@jbrowse/jexl';
 import { deserializeFilters } from './InfoFilterWidget/filterUtil';
 import { passesInfoFilters, passesSampleFilters } from '../../../utils';
 
@@ -27,6 +28,31 @@ function isUTR(feature: any) {
     )
 }
 
+function evaluateInfoFilters(feature: any, serializedFilters: any) {
+    try {
+        const filters = typeof serializedFilters === 'string'
+            ? JSON.parse(serializedFilters)
+            : serializedFilters
+        const expandedFilters = deserializeFilters(filters)
+        return passesInfoFilters(feature, expandedFilters)
+    } catch (e) {
+        console.error(e)
+        return true
+    }
+}
+
+function evaluateSampleFilters(feature: any, serializedSampleFilters: any) {
+    try {
+        const sampleFilters = typeof serializedSampleFilters === 'string'
+            ? JSON.parse(serializedSampleFilters)
+            : serializedSampleFilters
+        return passesSampleFilters(feature, sampleFilters)
+    } catch (e) {
+        console.error(e)
+        return true
+    }
+}
+
 export default class ExtendedVariantPlugin extends Plugin {
     name = 'ExtendedVariantPlugin'
     version = "0.0.1"
@@ -199,30 +225,10 @@ export default class ExtendedVariantPlugin extends Plugin {
             return val ? Number(val).toLocaleString() : val
         })
 
-        pluginManager.jexl.addFunction('passesInfoFilters', (feature, serializedFilters) => {
-            try {
-                const filters = typeof serializedFilters === 'string'
-                    ? JSON.parse(serializedFilters)
-                    : serializedFilters
-                const expandedFilters = deserializeFilters(filters)
-                return passesInfoFilters(feature, expandedFilters)
-            } catch (e) {
-                console.error(e)
-                return true
-            }
-        })
-
-        pluginManager.jexl.addFunction('passesSampleFilters', (feature, serializedSampleFilters) => {
-            try {
-                const sampleFilters = typeof serializedSampleFilters === 'string'
-                    ? JSON.parse(serializedSampleFilters)
-                    : serializedSampleFilters
-                return passesSampleFilters(feature, sampleFilters)
-            } catch (e) {
-                console.error(e)
-                return true
-            }
-        })
+        jexl.addFunction('passesInfoFilters', evaluateInfoFilters)
+        jexl.addFunction('passesSampleFilters', evaluateSampleFilters)
+        pluginManager.jexl.addFunction('passesInfoFilters', evaluateInfoFilters)
+        pluginManager.jexl.addFunction('passesSampleFilters', evaluateSampleFilters)
     }
 
     configure(pluginManager: PluginManager) {

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

@@ -84,7 +84,6 @@ public void testSteps() throws Exception
     {
         setUpTest();
 
-        testFullTextSearch();
         testInferredDetails();
         testNoSession();
         testMessageDisplay();