Merge pull request #778 from hms-dbmi-cellenics/check-file-size

[BIOMAGE-1774] Display spinner during sample validation

src/__test__/redux/actions/samples/createSample.test.js

@@ -7,6 +7,7 @@ import { v4 as uuidv4 } from 'uuid';
 import createSample from 'redux/actions/samples/createSample';
 import initialSampleState from 'redux/reducers/samples/initialState';
 import initialExperimentState, { experimentTemplate } from 'redux/reducers/experiments/initialState';
+import 'utils/upload/sampleValidator';
 
 import {
   SAMPLES_CREATE, SAMPLES_SAVING, SAMPLES_ERROR, SAMPLES_SAVED,
@@ -15,6 +16,7 @@ import {
 import endUserMessages from 'utils/endUserMessages';
 import pushNotificationMessage from 'utils/pushNotificationMessage';
 
+jest.mock('utils/upload/sampleValidator');
 pushNotificationMessage.mockImplementation(() => async () => { });
 
 enableFetchMocks();
@@ -26,6 +28,7 @@ const sampleUuid = 'abc123';
 uuidv4.mockImplementation(() => sampleUuid);
 
 const sampleName = 'test sample';
+const sample = {};
 
 describe('createSample action', () => {
   const experimentId = 'exp234';
@@ -62,7 +65,7 @@ describe('createSample action', () => {
   it('Works correctly with one file being uploaded', async () => {
     fetchMock.mockResponse(JSON.stringify({}), { url: 'mockedUrl', status: 200 });
 
-    const newUuid = await store.dispatch(createSample(experimentId, sampleName, mockType, ['matrix.tsv.gz']));
+    const newUuid = await store.dispatch(createSample(experimentId, sampleName, sample, mockType, ['matrix.tsv.gz']));
 
     // Returns a new sampleUuid
     expect(newUuid).toEqual(sampleUuid);
@@ -85,7 +88,7 @@ describe('createSample action', () => {
   it('Works correctly with many files being uploaded', async () => {
     fetchMock.mockResponse(JSON.stringify({}), { url: 'mockedUrl', status: 200 });
 
-    const newUuid = await store.dispatch(createSample(experimentId, sampleName, mockType, ['matrix.tsv.gz', 'features.tsv.gz', 'barcodes.tsv.gz']));
+    const newUuid = await store.dispatch(createSample(experimentId, sampleName, sample, mockType, ['matrix.tsv.gz', 'features.tsv.gz', 'barcodes.tsv.gz']));
 
     // Returns a new sampleUuid
     expect(newUuid).toEqual(sampleUuid);
@@ -110,7 +113,7 @@ describe('createSample action', () => {
 
     await expect(
       store.dispatch(
-        createSample(experimentId, sampleName, mockType, ['matrix.tsv.gz']),
+        createSample(experimentId, sampleName, sample, mockType, ['matrix.tsv.gz']),
       ),
     ).rejects.toThrow(endUserMessages.ERROR_CREATING_SAMPLE);
 
@@ -125,7 +128,7 @@ describe('createSample action', () => {
 
     await expect(
       store.dispatch(
-        createSample(experimentId, sampleName, 'unrecognizable type', ['matrix.tsv.gz', 'features.tsv.gz', 'barcodes.tsv.gz']),
+        createSample(experimentId, sampleName, sample, 'unrecognizable type', ['matrix.tsv.gz', 'features.tsv.gz', 'barcodes.tsv.gz']),
       ),
     ).rejects.toThrow('Sample technology unrecognizable type is not recognized');
   });

src/redux/actions/samples/createSample.js

@@ -13,10 +13,13 @@ import { METADATA_DEFAULT_VALUE } from 'redux/reducers/experiments/initialState'
 import { sampleTemplate } from 'redux/reducers/samples/initialState';
 
 import UploadStatus from 'utils/upload/UploadStatus';
+import pushNotificationMessage from 'utils/pushNotificationMessage';
+import validate from 'utils/upload/sampleValidator';
 
 const createSample = (
   experimentId,
   name,
+  sample,
   type,
   filesToUpload,
 ) => async (dispatch, getState) => {
@@ -52,6 +55,12 @@ const createSample = (
   } else {
     throw new Error(`Sample technology ${type} is not recognized`);
   }
+  const errors = await validate(sample);
+  if (errors && errors.length > 0) {
+    const errorMessage = `Error uploading sample ${name}.\n${errors.join('\n')}`;
+    pushNotificationMessage('error', errorMessage, 15);
+    throw new Error(errorMessage);
+  }
 
   filesToUpload.forEach((fileName) => {
     newSample.files[fileName] = { upload: { status: UploadStatus.UPLOADING } };

src/redux/actions/samples/createSampleFile.js

@@ -53,7 +53,7 @@ const createSampleFile = (
 
     return signedUrl;
   } catch (e) {
-    // Can't update the upload status becuase we didn't even get to create the sample file
+    // Can't update the upload status because we didn't even get to create the sample file
     handleError(e, endUserMessages.ERROR_BEGIN_SAMPLE_FILE_UPLOAD);
 
     throw e;

src/utils/upload/processUpload.js

@@ -4,14 +4,12 @@ import _ from 'lodash';
 import axios from 'axios';
 
 import { createSample, createSampleFile, updateSampleFileUpload } from 'redux/actions/samples';
-import validate from 'utils/upload/sampleValidator';
 
 import UploadStatus from 'utils/upload/UploadStatus';
 import loadAndCompressIfNecessary from 'utils/upload/loadAndCompressIfNecessary';
 import { inspectFile, Verdict } from 'utils/upload/fileInspector';
 
 import getFileTypeV2 from 'utils/getFileTypeV2';
-import pushNotificationMessage from 'utils/pushNotificationMessage';
 
 const putInS3 = async (loadedFileData, signedUrl, onUploadProgress) => (
   await axios.request({
@@ -131,22 +129,15 @@ const processUpload = async (filesList, sampleType, samples, experimentId, dispa
   }, {});
 
   Object.entries(samplesMap).forEach(async ([name, sample]) => {
-    const errors = await validate(sample);
-
     const filesToUploadForSample = Object.keys(sample.files);
 
-    if (errors && errors.length > 0) {
-      const errorMessage = errors.join('\n');
-      pushNotificationMessage('error', `Error uploading sample ${name}.\n${errorMessage}`, 15);
-      return;
-    }
-
     // Create sample if not exists.
     try {
       sample.uuid ??= await dispatch(
         createSample(
           experimentId,
           name,
+          sample,
           sampleType,
           filesToUploadForSample,
         ),