Serialize variantTable location to variantSearch URL parameters

Author: Sebastian Benjamin

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

@@ -307,11 +307,6 @@ const VariantTableWidget = observer(props => {
 
     const showDetailsWidget = (rowIdx: number, params: any) => {
         (async () => {
-            /*let a = adapter;
-
-            if (!a) {
-                a = await getAdapterInstance();
-            }*/
             let a = await getAdapterInstance();
 
             const row = features[rowIdx] as any

jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx

@@ -5,6 +5,7 @@ import { createTheme } from '@mui/material/styles';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { ThemeProvider } from '@mui/material';
+import { parseLocString } from '@jbrowse/core/util';
 import LogSession from '../Browser/plugins/LogSession/index';
 import ExtendedVariantPlugin from '../Browser/plugins/ExtendedVariantPlugin/index';
 import VariantTableWidget from './components/VariantTableWidget';
@@ -35,6 +36,7 @@ function VariantTable() {
     const [state, setState] = useState(null);
     const [theme, setTheme] = useState(null);
     const [view, setView] = useState(null);
+    const [parsedLocString, setParsedLocString] = useState(null)
     const [pluginManager, setPluginManager] = useState(null);
     const [assembly, setAssembly] = useState<Assembly>(null);
     const [assemblyName, setAssemblyName] = useState<string>(null)
@@ -54,6 +56,15 @@ function VariantTable() {
             setPluginManager(pluginManager)
             setState(state)
 
+            const isValidRefNameForAssembly = function(refName: string, assemblyName?: string) {
+                return assemblyManager.isValidRefName(refName, assemblyNames[0])
+            }
+
+            if (locString) {
+                const parsedLocString = parseLocString(locString, isValidRefNameForAssembly)
+                setParsedLocString(parsedLocString)
+            }
+
             // @ts-ignore
             setTheme(createJBrowseTheme(readConfObject(state.config.configuration, 'theme')))
         }
@@ -80,7 +91,7 @@ function VariantTable() {
                 <ErrorBoundary>
                     <JBrowseFilterPanel session={state.session}/>
                     <VariantTableWidget assembly={assembly} assemblyName={assemblyName} trackId={trackId} locString={locString}
-                                        sessionId={sessionId} session={session} pluginManager={pluginManager}/>
+                                        sessionId={sessionId} session={session} pluginManager={pluginManager} parsedLocString={parsedLocString}/>
                 </ErrorBoundary>
             </div>
         </ThemeProvider>

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

@@ -37,7 +37,7 @@ import { ActionURL, Ajax } from '@labkey/api';
 import { deserializeFilters } from '../../Browser/plugins/ExtendedVariantPlugin/InfoFilterWidget/filterUtil';
 
 const VariantTableWidget = observer(props => {
-  const { assembly, assemblyName, trackId, locString, sessionId, session, pluginManager } = props
+  const { assembly, assemblyName, trackId, locString, parsedLocString, sessionId, session, pluginManager } = props
   const { view, assemblyManager } = session
 
   const isValidRefNameForAssembly = function(refName: string, assemblyName?: string) {
@@ -78,7 +78,7 @@ const VariantTableWidget = observer(props => {
         navigateToBrowser(sessionId, locString, trackId, track)
         break;
       case "luceneRedirect":
-        navigateToSearch(sessionId, locString, trackId, track)
+        navigateToSearch(sessionId, locString, parsedLocString, trackId, track)
         break;
     }
   }

jbrowse/src/client/JBrowse/utils.ts

@@ -223,10 +223,14 @@ export function navigateToTable(sessionId, locString, trackId, track?: any) {
     window.location.href = ActionURL.buildURL("jbrowse", "variantTable.view", null, {session: sessionId, location: locString, trackId: trackId, activeTracks: trackId, sampleFilters: sampleFilterURL, infoFilters: infoFilterURL})
 }
 
-export function navigateToSearch(sessionId, locString, trackId, track?: any) {
+export function navigateToSearch(sessionId, locString, parsedLocString: ParsedLocString, trackId, track?: any) {
     const sampleFilterURL = serializeSampleFilters(track)
     const infoFilterURL = serializeInfoFilters(track)
-    window.location.href = ActionURL.buildURL("jbrowse", "variantSearch.view", null, {session: sessionId, location: locString, trackId: trackId, activeTracks: trackId, sampleFilters: sampleFilterURL, infoFilters: infoFilterURL})
+
+    const contig = parsedLocString.refName;
+    const start = parsedLocString.start;
+    const end = parsedLocString.end;
+    window.location.href = ActionURL.buildURL("jbrowse", "variantSearch.view", null, {session: sessionId, location: locString, trackId: trackId, activeTracks: trackId, sampleFilters: sampleFilterURL, infoFilters: infoFilterURL, searchString: serializeLocationToLuceneQuery(contig, start, end)})
 }
 
 export function navigateToBrowser(sessionId: string, locString: string, trackGUID?: string, track?: any) {
@@ -301,6 +305,16 @@ 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) {
+    const filters = [
+        {field: "contig", operator: "equals", value: contig.toString()},
+        {field: "start", operator: ">=", value: start.toString()},
+        {field: "end", operator: "<=", value: end.toString()}
+    ]
+
+    return createEncodedFilterString(filters, false)
+}
+
 function generateLuceneString(field, operator, value) {
   let luceneQueryString = '';