Merge pull request #956 from biomage-org/65-restrict-upload-status-ch…

…anges

Restrict upload status changes

src/__test__/components/data-management/SamplesTableCells.test.jsx

@@ -13,7 +13,7 @@ import {
 } from 'components/data-management/SamplesTableCells';
 import UploadStatus, { messageForStatus } from 'utils/upload/UploadStatus';
 import { makeStore } from 'redux/store';
-import mockAPI, { generateDefaultMockAPIResponses } from '__test__/test-utils/mockAPI';
+import mockAPI, { generateDefaultMockAPIResponses, statusResponse } from '__test__/test-utils/mockAPI';
 import { loadSamples, updateSampleFileUpload } from 'redux/actions/samples';
 
 import fake from '__test__/test-utils/constants';
@@ -40,6 +40,7 @@ jest.mock('swr', () => () => ({
 
 const experimentId = `${fake.EXPERIMENT_ID}-0`;
 const sampleId = `${fake.SAMPLE_ID}-0`;
+const sampleFileId = `${fake.SAMPLE_FILE_ID}`;
 
 enableFetchMocks();
 
@@ -50,7 +51,10 @@ describe('UploadCell', () => {
 
   beforeEach(async () => {
     fetchMock.mockClear();
-    fetchMock.mockIf(/.*/, mockAPI(generateDefaultMockAPIResponses(experimentId)));
+    fetchMock.mockIf(/.*/, mockAPI({
+      [`experiments/${experimentId}/sampleFiles/${sampleFileId}$`]: () => statusResponse(200, 'OK'),
+      ...generateDefaultMockAPIResponses(experimentId),
+    }));
 
     storeState = makeStore();
 
@@ -73,7 +77,7 @@ describe('UploadCell', () => {
 
     await storeState.dispatch(
       updateSampleFileUpload(
-        experimentId, sampleId, 'features10x', UploadStatus.UPLOADING, percentUploaded,
+        experimentId, sampleId, sampleFileId, 'features10x', UploadStatus.UPLOADING, percentUploaded,
       ),
     );
 

src/__test__/test-utils/constants.js

@@ -6,6 +6,7 @@ export default {
   EXPERIMENT_NAME: 'Test Experiment',
   PROJECT_ID: 'test24b6-8600-test-mock-63822d2fmock',
   SAMPLE_ID: 'test9188-d682-test-mock-cb6d644cmock',
+  SAMPLE_FILE_ID: 'test4321-1234-test-mock-sampfilemock',
   API_ENDPOINT: /^http?:\/\/localhost:3000.*$/,
   S3_ENDPOINT: 'http://mock.s3.amazonaws.com',
   // pragma: allowlist secret

src/__test__/utils/upload/__snapshots__/process10XUpload.test.js.snap

@@ -73,7 +73,7 @@ exports[`processUpload Should not upload files if there are errors beginning the
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/features10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploadError"}",
       "headers": {
@@ -83,7 +83,7 @@ exports[`processUpload Should not upload files if there are errors beginning the
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/barcodes10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploadError"}",
       "headers": {
@@ -93,7 +93,7 @@ exports[`processUpload Should not upload files if there are errors beginning the
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/matrix10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploadError"}",
       "headers": {
@@ -193,7 +193,7 @@ exports[`processUpload Updates redux correctly when there are file upload errors
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/features10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploadError"}",
       "headers": {
@@ -203,7 +203,7 @@ exports[`processUpload Updates redux correctly when there are file upload errors
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/barcodes10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploadError"}",
       "headers": {
@@ -213,7 +213,7 @@ exports[`processUpload Updates redux correctly when there are file upload errors
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/matrix10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploadError"}",
       "headers": {
@@ -363,7 +363,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/features10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploaded"}",
       "headers": {
@@ -373,7 +373,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/barcodes10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploaded"}",
       "headers": {
@@ -383,7 +383,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/matrix10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploaded"}",
       "headers": {
@@ -533,7 +533,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/features10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploaded"}",
       "headers": {
@@ -543,7 +543,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/barcodes10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploaded"}",
       "headers": {
@@ -553,7 +553,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
   ],
   [
-    "http://localhost:3000/v2/experiments/project-uuid/samples/mockSampleId/sampleFiles/matrix10x",
+    "http://localhost:3000/v2/experiments/project-uuid/sampleFiles/mockSampleFileId",
     {
       "body": "{"uploadStatus":"uploaded"}",
       "headers": {

src/__test__/utils/upload/process10XUpload.test.js

@@ -140,10 +140,16 @@ const mockProcessUploadCalls = () => {
       result = { status: 200, body: JSON.stringify({ WT13: sampleId }) };
     }
 
+    // Create sample file
     if (new RegExp(`/v2/experiments/${mockExperimentId}/samples/.*/sampleFiles/.*`).test(url)) {
       result = { status: 200, body: JSON.stringify({}) };
     }
 
+    // Update sample file status
+    if (new RegExp(`/v2/experiments/${mockExperimentId}/sampleFiles/.*`).test(url)) {
+      result = { status: 200, body: JSON.stringify({}) };
+    }
+
     if (url.endsWith(`/v2/experiments/${mockExperimentId}/sampleFiles/${sampleFileId}/beginUpload`)) {
       result = { status: 200, body: JSON.stringify(mockUploadUrlParams) };
     }

src/components/data-management/metadata/AddMetadataButton.jsx

@@ -59,7 +59,7 @@ const AddMetadataButton = ({ samplesTableRef }) => {
     }
 
     try {
-      await prepareAndUploadFileToS3(file, uploadUrlParams, 'cellLevelMeta', onUpdateUploadStatus);
+      await prepareAndUploadFileToS3(file, uploadUrlParams, 'cellLevelMeta', new AbortController(), onUpdateUploadStatus);
     } catch (e) {
       pushNotificationMessage('error', 'Something went wrong while uploading your metadata file.');
       console.log(e);

src/redux/actions/samples/createSampleFile.js

@@ -17,10 +17,12 @@ const createSampleFile = (
 ) => async (dispatch) => {
   const updatedAt = dayjs().toISOString();
 
+  const sampleFileId = uuidv4();
+
   try {
     const url = `/v2/experiments/${experimentId}/samples/${sampleId}/sampleFiles/${type}`;
     const body = {
-      sampleFileId: uuidv4(),
+      sampleFileId,
       size: fileForApiV1.size,
     };
 
@@ -52,7 +54,9 @@ const createSampleFile = (
 
     return body.sampleFileId;
   } catch (e) {
-    dispatch(updateSampleFileUpload(experimentId, sampleId, type, UploadStatus.UPLOAD_ERROR));
+    dispatch(updateSampleFileUpload(
+      experimentId, sampleId, sampleFileId, type, UploadStatus.UPLOAD_ERROR,
+    ));
 
     throw e;
   }

src/redux/actions/samples/updateSampleFileUpload.js

@@ -8,14 +8,14 @@ import UploadStatus from 'utils/upload/UploadStatus';
 import fileNameForApiV1 from 'utils/upload/fileNameForApiV1';
 
 const updateSampleFileUpload = (
-  experimentId, sampleId, type, uploadStatus, uploadProgress,
+  experimentId, sampleId, sampleFileId, type, uploadStatus, uploadProgress,
 ) => async (dispatch) => {
   const updatedAt = dayjs().toISOString();
 
   // Don't send an api update whenever the progress bar is updated, only for uploadStatus changes
   // TODO: move progress to not even be a part of redux, manage it in a different way
   if (uploadStatus !== UploadStatus.UPLOADING) {
-    const url = `/v2/experiments/${experimentId}/samples/${sampleId}/sampleFiles/${type}`;
+    const url = `/v2/experiments/${experimentId}/sampleFiles/${sampleFileId}`;
     const body = { uploadStatus };
 
     try {

src/utils/upload/processMultipartUpload.js

@@ -4,7 +4,7 @@ const FILE_CHUNK_SIZE = 10000000;
 const MAX_RETRIES = 2;
 
 const putPartInS3 = async (
-  blob, signedUrl, onUploadProgress, currentRetry = 0, abortController = null,
+  blob, signedUrl, onUploadProgress, abortController, currentRetry = 0,
 ) => {
   try {
     return await axios.request({
@@ -19,7 +19,9 @@ const putPartInS3 = async (
     });
   } catch (e) {
     if (currentRetry < MAX_RETRIES) {
-      return await putPartInS3(blob, signedUrl, onUploadProgress, currentRetry + 1);
+      return await putPartInS3(
+        blob, signedUrl, onUploadProgress, abortController, currentRetry + 1,
+      );
     }
 
     throw e;
@@ -42,8 +44,8 @@ const processMultipartUpload = async (
       blob,
       signedUrl,
       createOnUploadProgressForPart(index),
-      0,
       abortController,
+      0,
     );
 
     promises.push(req);

src/utils/upload/processUpload.js

@@ -18,7 +18,7 @@ import endUserMessages from 'utils/endUserMessages';
 import pushNotificationMessage from 'utils/pushNotificationMessage';
 
 const prepareAndUploadFileToS3 = async (
-  file, uploadUrlParams, type, onStatusUpdate = () => { }, abortController = null,
+  file, uploadUrlParams, type, abortController, onStatusUpdate = () => { },
 ) => {
   let parts = null;
   const { signedUrls, uploadId, fileId } = uploadUrlParams;
@@ -89,7 +89,7 @@ const createAndUploadSampleFile = async (file, experimentId, sampleId, dispatch,
     try {
       file.fileObject = await loadAndCompressIfNecessary(file, () => {
         dispatch(updateSampleFileUpload(
-          experimentId, sampleId, fileType, UploadStatus.COMPRESSING,
+          experimentId, sampleId, sampleFileId, fileType, UploadStatus.COMPRESSING,
         ));
       });
 
@@ -99,7 +99,9 @@ const createAndUploadSampleFile = async (file, experimentId, sampleId, dispatch,
         ? UploadStatus.FILE_READ_ABORTED
         : UploadStatus.FILE_READ_ERROR;
 
-      dispatch(updateSampleFileUpload(experimentId, sampleId, fileType, fileErrorStatus));
+      dispatch(updateSampleFileUpload(
+        experimentId, sampleId, sampleFileId, fileType, fileErrorStatus,
+      ));
       return;
     }
   }
@@ -114,15 +116,15 @@ const createAndUploadSampleFile = async (file, experimentId, sampleId, dispatch,
 
     const updateSampleFileUploadProgress = (status, percentProgress = 0) => dispatch(
       updateSampleFileUpload(
-        experimentId, sampleId, fileType, status, percentProgress,
+        experimentId, sampleId, sampleFileId, fileType, status, percentProgress,
       ),
     );
 
     const uploadUrlParams = { signedUrls, uploadId, fileId: sampleFileId };
-    await prepareAndUploadFileToS3(file, uploadUrlParams, 'sample', updateSampleFileUploadProgress, abortController);
+    await prepareAndUploadFileToS3(file, uploadUrlParams, 'sample', abortController, updateSampleFileUploadProgress);
   } catch (e) {
     dispatch(updateSampleFileUpload(
-      experimentId, sampleId, fileType, UploadStatus.UPLOAD_ERROR,
+      experimentId, sampleId, sampleFileId, fileType, UploadStatus.UPLOAD_ERROR,
     ));
   }
 };