Study page clinical data tab: fix download after pagination change

src/pages/studyView/StudyViewPageStore.ts

@@ -9790,11 +9790,42 @@ export class StudyViewPageStore
  if (this.selectedSamples.result.length === 0) {
  return Promise.resolve('');
  }
- let sampleClinicalDataResponse = await getAllClinicalDataByStudyViewFilter(
- this.filters,
- undefined,
- undefined
- );
+
+ const BATCH_SIZE = 25000;
+
+ const getBatch = (page: number) =>
+ getAllClinicalDataByStudyViewFilter(
+ this.filters,
+ undefined,
+ undefined,
+ 'desc',
+ BATCH_SIZE,
+ page
+ );
+
+ // get first page, which gives us the total count, which we can use to figure out how many pages
+ // we need to download
+ let sampleClinicalDataResponse = await getBatch(0);
+
+ // create a target object to merge batches onto
+ // the results are { sampleId: clinicaldData[] }
+ // where the counted "rows" are samples. So a count of 1000 means you getting all clinical data from 1000
+ // samples, grouped by sampleId
+ const resultObj = { ...sampleClinicalDataResponse.data };
+
+ // if there are more than one batch, we need to fetch them and merge them into result
+ if (sampleClinicalDataResponse.totalItems > BATCH_SIZE) {
+ const pages = Math.ceil(
+ sampleClinicalDataResponse.totalItems / BATCH_SIZE
+ );
+ // start at one because we already have the first page from the initial fetch up above
+ let i = 1;
+ do {
+ const batch = await getBatch(i);
+ i++;
+ Object.assign(resultObj, batch.data);
+ } while (i < pages);
+ }
 
  let clinicalAttributesNameSet = _.reduce(
  this.clinicalAttributes.result,
@@ -9818,8 +9849,7 @@ export class StudyViewPageStore
  patientId: next.patientId,
  sampleId: next.sampleId,
  } as { [attributeId: string]: string };
- const clinicalData =
- sampleClinicalDataResponse.data[next.uniqueSampleKey];
+ const clinicalData = resultObj[next.uniqueSampleKey];
  _.forEach(
  clinicalData,
  (attr: ClinicalData) =>

src/pages/studyView/StudyViewUtils.tsx

@@ -3158,7 +3158,8 @@ export async function getAllClinicalDataByStudyViewFilter(
  searchTerm: string | undefined,
  sortAttributeId: any,
  sortDirection: any = 'asc',
- pageSize: number = 500
+ pageSize: number,
+ pageNumber: number
 ): Promise<{
  totalItems: number;
  data: { [uniqueSampleKey: string]: ClinicalData[] };
@@ -3169,8 +3170,8 @@ export async function getAllClinicalDataByStudyViewFilter(
  ] = await internalClient
  .fetchClinicalDataClinicalTableUsingPOSTWithHttpInfo({
  studyViewFilter,
- pageSize,
- pageNumber: 0,
+ pageSize: pageSize | 500,
+ pageNumber: pageNumber || 0,
  searchTerm: searchTerm,
  sortBy: sortAttributeId,
  direction: sortDirection?.toUpperCase(),

src/pages/studyView/tabs/ClinicalDataTab.tsx

@@ -64,7 +64,8 @@ async function fetchClinicalDataForStudyViewClinicalDataTab(
  searchTerm,
  sortAttributeId,
  sortDirection,
- recordLimit
+ recordLimit,
+ 0
  );
 
  const aggregatedSampleClinicalData = _.mapValues(