Merge branch 'master' of github.com:biomage-org/ui into refactor-etag

Signed-off-by: Pol Alvarez <[email protected]>
hms-dbmi-cellenics · Oct 25, 2023 · a313509 · a313509
2 parents 0cc687f + 3a97656
commit a313509
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Showing 7 changed files with 9 additions and 48 deletions.
diff --git a/...test__/pages/experiments/[experimentId]/plots-and-tables/normalized-matrix/index.test.jsx b/...test__/pages/experiments/[experimentId]/plots-and-tables/normalized-matrix/index.test.jsx
@@ -112,7 +112,7 @@ describe('Normalized matrix index page', () => {
 
     await waitFor(() => {
       expect(writeToFileURL).toHaveBeenCalledWith(result);
-      expect(downloadFromUrl).toHaveBeenCalledWith(writeToFileURLResult, 'NormalizedExpression.csv');
+      expect(downloadFromUrl).toHaveBeenCalledWith(writeToFileURLResult, 'NormalizedExpression.csv.gz');
     });
   });
 
@@ -159,7 +159,7 @@ describe('Normalized matrix index page', () => {
 
     await waitFor(() => {
       expect(writeToFileURL).toHaveBeenCalledWith(result);
-      expect(downloadFromUrl).toHaveBeenCalledWith(writeToFileURLResult, 'NormalizedExpression.csv');
+      expect(downloadFromUrl).toHaveBeenCalledWith(writeToFileURLResult, 'NormalizedExpression.csv.gz');
     });
   });
 

diff --git a/src/redux/actions/componentConfig/downloadNormalizedMatrix.js b/src/redux/actions/componentConfig/downloadNormalizedMatrix.js
@@ -28,7 +28,7 @@ const downloadNormalizedMatrix = (
       dispatch,
     );
 
-    downloadFromUrl(writeToFileURL(data), 'NormalizedExpression.csv');
+    downloadFromUrl(writeToFileURL(data), 'NormalizedExpression.csv.gz');
 
     dispatch({
       type: PLOT_DATA_LOADED,

diff --git a/src/utils/getTimeoutForWorkerTask.js b/src/utils/getTimeoutForWorkerTask.js
@@ -13,7 +13,8 @@ const getTimeoutForWorkerTask = (state, taskName) => {
   switch (taskName) {
     case 'GetEmbedding':
     case 'ListGenes':
-    case 'MarkerHeatmap': {
+    case 'MarkerHeatmap':
+    case 'GetNormalizedExpression': {
       // all of this calls can happen at the same time and each of them can potentially have to
       // wait for the others to finish before it starts processing (due to the SQS) so the timeout
       // needs to be large enough for the slowest task to finish
@@ -36,7 +37,6 @@ const getTimeoutForWorkerTask = (state, taskName) => {
     case 'GeneExpression':
     case 'GetMitochondrialContent':
     case 'GetDoubletScore':
-    case 'GetNormalizedExpression':
     case 'DownloadAnnotSeuratObject':
     case 'DifferentialExpression':
     case 'GetNUmis':

diff --git a/src/utils/work/dispatchWorkRequest.js b/src/utils/work/dispatchWorkRequest.js
@@ -49,7 +49,7 @@ const dispatchWorkRequest = async (
 
   console.log('dispatching work request', request);
   // TODO test what happens when api throws an error here
-  const response = await fetchAPI(
+  const { data: { ETag, signedUrl } } = await fetchAPI(
     `/v2/workRequest/${experimentId}`,
     {
       method: 'POST',
@@ -58,8 +58,6 @@ const dispatchWorkRequest = async (
     },
   );
 
-  console.log('work request response', response);
-  const { data: { ETag, signedUrl } } = response;
   return { ETag, signedUrl, request };
 };
 

diff --git a/src/utils/work/fetchWork.js b/src/utils/work/fetchWork.js
@@ -5,44 +5,6 @@ import dispatchWorkRequest from 'utils/work/dispatchWorkRequest';
 import downloadFromS3 from 'utils/work/downloadFromS3';
 import waitForWorkRequest from './waitForWorkRequest';
 
-// Temporarily using gene expression without local cache
-// const fetchGeneExpressionWorkWithoutLocalCache = async (
-//   experimentId,
-//   timeout,
-//   body,
-//   backendStatus,
-//   environment,
-//   broadcast,
-//   extras,
-//   dispatch,
-// ) => {
-//   // If new genes are needed, construct payload, try S3 for results,
-//   // and send out to worker if there's a miss.
-//   const { pipeline: { startDate: qcPipelineStartDate } } = backendStatus;
-
-//   // const ETag = await generateETag(
-//   //   experimentId,
-//   //   body,
-//   //   extras,
-//   //   qcPipelineStartDate,
-//   //   environment,
-//   //   dispatch,
-//   //   getState,
-//   // );
-
-//   const { ETag, signedUrl, data } = await sendWorkRequest(
-//     experimentId,
-//     body,
-//     timeout,
-//     {
-//       broadcast,
-//       ...extras,
-//     },
-//     dispatch,
-//   );
-
-//   return data ?? await downloadFromS3(body.name, signedUrl);
-// };
 // retrieveData will try to get the data for the given experimentId and ETag from
 // the fastest source possible. It will try to get the data in order from:
 // 1. Browser cache

diff --git a/src/utils/work/unpackResult.js b/src/utils/work/unpackResult.js
@@ -2,7 +2,7 @@ import { decompress } from 'fflate';
 
 const unpackResult = async (storageResp, taskName = null) => {
   // SeuratObject can fail to download when loaded into memory
-  if (taskName === 'DownloadAnnotSeuratObject') {
+  if (taskName === 'DownloadAnnotSeuratObject' || taskName === 'GetNormalizedExpression') {
     const blob = await storageResp.blob();
     return (blob);
   }

diff --git a/src/utils/work/waitForWorkRequest.js b/src/utils/work/waitForWorkRequest.js
@@ -47,7 +47,8 @@ const getWorkerTimeout = (taskName, defaultTimeout) => {
   switch (taskName) {
     case 'GetEmbedding':
     case 'ListGenes':
-    case 'MarkerHeatmap': {
+    case 'MarkerHeatmap':
+    case 'GetNormalizedExpression': {
       return dayjs().add(1800, 's').toISOString();
     }