Fix URL encoding behavior and tests

Author: Sebastian Benjamin

jbrowse/src/client/JBrowse/VariantSearch/components/VariantTableWidget.tsx

@@ -13,6 +13,7 @@ import {
     GridToolbarExport
 } from '@mui/x-data-grid';
 import SearchIcon from '@mui/icons-material/Search';
+import { OperatorKey } from '../operators'
 import LinkIcon from '@mui/icons-material/Link';
 import DownloadIcon from '@mui/icons-material/Download'
 import { ActionURL } from '@labkey/api';
@@ -99,7 +100,7 @@ const VariantTableWidget = observer(props => {
     const handleExport = () => {
         const currentUrl = new URL(window.location.href);
 
-        const searchString = buildLuceneQuery(filters);
+        const searchString = encodeURIComponent(buildLuceneQuery(filters));
         const sortField = sortModel[0]?.field ?? 'genomicPosition';
         const sortDirection = sortModel[0]?.sort ?? false;
 
@@ -553,7 +554,7 @@ const VariantTableWidget = observer(props => {
             <div style={{ marginBottom: "10px", display: "flex", alignItems: "center" }}>
                 <div style={{ flex: 1 }}>
                     {filters.map((filter, index) => {
-                        if ((filter as any).field && ((filter as any).operator === "is empty" || (filter as any).operator === "is not empty") && !(filter as any).value) {
+                        if ((filter as any).field && ((filter as any).operator.key === OperatorKey.IsEmpty || (filter as any).operator.key === OperatorKey.IsNotEmpty) && !(filter as any).value) {
                             return (
                                 <Button
                                     key={index}

jbrowse/src/client/JBrowse/VariantSearch/operators.ts

@@ -31,8 +31,15 @@ export interface Operator<T extends Value = Value> {
   generateLucene(field: string, value: T): string
 }
 
-function fuzzyNumRange(field: string, v: number) {
-  return `[${v - 0.000001} TO ${v + 0.000001}]`
+function fuzzyNumRange(field: string, raw: string | number) {
+  const floatValue = parseFloat(String(raw))
+  const intValue   = parseInt(String(raw), 10)
+
+  if (floatValue === intValue) {
+    return `[${intValue} TO ${intValue}]`
+  }
+
+  return `[${floatValue - 0.000001} TO ${floatValue + 0.000001}]`
 }
 
 export const OperatorRegistry: Record<OperatorKey, Operator> = {

jbrowse/src/client/JBrowse/utils.ts

@@ -240,7 +240,7 @@ export function navigateToSearch(sessionId, locString, trackId, isValidRefNameFo
         const start = parsedLocString.start;
         const end = parsedLocString.end;
 
-        searchString = serializeLocationToLuceneQuery(contig, start, end)
+        searchString = serializeLocationToEncodedSearchString(contig, start, end)
     }
 
     window.location.href = ActionURL.buildURL("jbrowse", "variantSearch.view", null, {session: sessionId, location: locString, trackId: trackId, activeTracks: trackId, sampleFilters: sampleFilterURL, infoFilters: infoFilterURL, searchString: searchString})
@@ -318,7 +318,7 @@ export function getGenotypeURL(trackId, contig, start, end) {
     return ActionURL.buildURL("jbrowse", "genotypeTable.view", null, {trackId: trackId, chr: contig, start: start, stop: end})
 }
 
-export function serializeLocationToLuceneQuery(contig, start, end) {
+export function serializeLocationToEncodedSearchString(contig, start, end) {
     const filters = [
         new Filter("contig", OperatorKey.Equals, contig.toString()),
         new Filter("start", OperatorKey.NumericGte, start.toString()),
@@ -348,6 +348,9 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
         return
     }
 
+    const lucene = buildLuceneQuery(filters)
+    const encoded = encodeURIComponent(lucene)
+
     let sortReverse;
     if(sortReverseString == "asc") {
         sortReverse = true
@@ -366,7 +369,7 @@ export async function fetchLuceneQuery(filters, sessionId, trackGUID, offset, pa
             failureCallback("There was an error: " + res.status + "\n Status Body: " + res.responseText + "\n Session ID:" + sessionId)
         },
         params: {
-            "searchString": buildLuceneQuery(filters),
+            "searchString": encoded,
             "sessionId": sessionId,
             "trackId": trackGUID,
             "offset": offset,
@@ -513,11 +516,11 @@ export function createEncodedFilterString(filters: Filter[]): string {
 }
 
 export function buildLuceneQuery(filters: Filter[]): string {
-    if (!filters.length || filters.every(f => f.isEmpty())) return 'all'
-    return filters
-        .filter(f => !f.isEmpty())
-        .map(f => f.toLucene())
-        .join('&')
+  if (!filters.length || filters.every(f => f.isEmpty())) return 'all'
+  return filters
+      .filter(f => !f.isEmpty())
+      .map(f => f.toLucene())
+      .join('&')
 }
 
 export async function fetchFieldTypeInfo(sessionId: string, trackId: string, successCallback: (fields: FieldModel[], groups: string[], promotedFilters: Map<string, Filter[]>) => void, failureCallback) {