Preserve merged-track OQL groups when submitting queries from Study View

src/pages/studyView/StudyViewPageStore.ts

@@ -196,6 +196,7 @@ import {
     getDefaultClinicalDataBinFilter,
     getCustomChartDownloadData,
     generateColorMapKey,
+    getGeneListForStudyViewSubmission,
     MutationCategorization,
     getChartMetaSet,
     getVisibleAttributes,
@@ -10350,9 +10351,10 @@ export class StudyViewPageStore
         let url = '/';
         if (!_.isEmpty(this.geneQueries)) {
             formOps.Action = 'Submit';
-            formOps.gene_list = this.geneQueries
-                .map(query => unparseOQLQueryLine(query))
-                .join('\n');
+            formOps.gene_list = getGeneListForStudyViewSubmission(
+                this.geneQueryStr,
+                this.geneQueries
+            );
             url = '/results';
         }
         submitToPage(url, formOps, '_blank');

src/pages/studyView/StudyViewUtils.spec.tsx

@@ -37,6 +37,7 @@ import {
     getExponent,
     getFilteredMolecularProfilesByAlterationType,
     getFilteredSampleIdentifiers,
+    getGeneListForStudyViewSubmission,
     getFilteredStudiesWithSamples,
     getFrequencyStr,
     getGroupedClinicalDataByBins,
@@ -4846,6 +4847,29 @@ describe('StudyViewUtils', () => {
         });
     });
 
+    describe('getGeneListForStudyViewSubmission', () => {
+        it('keeps merged-track OQL query text unchanged', () => {
+            const mergedTrackQuery =
+                '["My fav genes"  TP53: HOMDEL, BRAF: V600E]';
+            assert.strictEqual(
+                getGeneListForStudyViewSubmission(mergedTrackQuery, [
+                    { gene: 'TP53', alterations: [{ alteration_type: 'homdel' }] },
+                    { gene: 'BRAF', alterations: [{ alteration_type: 'mut' }] },
+                ] as SingleGeneQuery[]),
+                mergedTrackQuery
+            );
+        });
+
+        it('falls back to parsed query list when query text is empty', () => {
+            assert.strictEqual(
+                getGeneListForStudyViewSubmission('', [
+                    { gene: 'TP53', alterations: false },
+                ] as SingleGeneQuery[]),
+                'TP53'
+            );
+        });
+    });
+
     describe('annotationFilterActive', () => {
         it('false when all excluded', () => {
             assert.isFalse(annotationFilterActive(false, false, false));

src/pages/studyView/StudyViewUtils.tsx

@@ -119,7 +119,10 @@ import {
     GenomicDataCountFilter,
     GenomicDataFilter,
 } from 'cbioportal-ts-api-client/dist/generated/CBioPortalAPIInternal';
-import { queryContainsStructVarAlteration } from 'shared/lib/oql/oqlfilter';
+import {
+    queryContainsStructVarAlteration,
+    unparseOQLQueryLine,
+} from 'shared/lib/oql/oqlfilter';
 import { toast } from 'react-toastify';
 import { useCallback } from 'react';
 import { MutationOptionConstants } from 'shared/constants';
@@ -597,6 +600,17 @@ export function updateGeneQuery(
     return updatedQueries;
 }
 
+export function getGeneListForStudyViewSubmission(
+    geneQueryStr: string,
+    geneQueries: SingleGeneQuery[]
+): string {
+    const normalizedGeneQueryStr = geneQueryStr.trim();
+    if (normalizedGeneQueryStr.length > 0) {
+        return normalizedGeneQueryStr;
+    }
+    return geneQueries.map(query => unparseOQLQueryLine(query)).join('\n');
+}
+
 function translateSpecialText(text: string | undefined): string {
     if (!text) {
         return '';