Merge branch 'master' into send-embedding-method

src/__test__/components/data-processing/data-integration/DataIntegration.test.jsx

@@ -1,7 +1,9 @@
 import React from 'react';
 import { Provider } from 'react-redux';
 import '__test__/test-utils/setupTests';
-import { screen, render, waitFor } from '@testing-library/react';
+import {
+  screen, render, waitFor, within,
+} from '@testing-library/react';
 import userEvent from '@testing-library/user-event';
 import _ from 'lodash';
 import fake from '__test__/test-utils/constants';
@@ -204,4 +206,31 @@ describe('DataIntegration', () => {
     // The legend alert plot text should appear
     expect(screen.getByText(/We have hidden the plot legend, because it is too large and it interferes with the display of the plot/)).toBeInTheDocument();
   });
+
+  it('Renders the elbow plot by default when the experiment is single sample', async () => {
+    // Remove all sample other than the first one.
+    // This way, getIsUnisample() will detect the exp as unisample
+    const unisampleCellSetsData = _.cloneDeep(cellSetsData);
+    _.find(unisampleCellSetsData.cellSets, { key: 'sample' }).children.splice(1);
+
+    const mockSingleSampleApiResponses = {
+      ...generateDefaultMockAPIResponses(fake.EXPERIMENT_ID),
+      [`experiments/${fake.EXPERIMENT_ID}/cellSets$`]: () => promiseResponse(
+        JSON.stringify(unisampleCellSetsData),
+      ),
+    };
+
+    fetchMock
+      .mockReset()
+      .mockIf(/.*/, mockAPI(mockSingleSampleApiResponses));
+
+    storeState = makeStore();
+    await storeState.dispatch(loadBackendStatus(fake.EXPERIMENT_ID));
+    await storeState.dispatch(loadProcessingSettings(fake.EXPERIMENT_ID));
+    await storeState.dispatch(loadCellSets(fake.EXPERIMENT_ID));
+
+    await renderDataIntegration(storeState);
+
+    expect(screen.getByRole('radio', { name: 'Elbow plot showing principal components' })).toBeChecked();
+  });
 });

src/__test__/redux/reducers/samplesReducer.test.js

@@ -398,4 +398,18 @@ describe('samplesReducer', () => {
 
     expect(newState).toMatchSnapshot();
   });
+
+  it('Sample file update doesnt change anything if the sample no longer exists', () => {
+    const newState = samplesReducer(initialState, {
+      type: SAMPLES_FILE_UPDATE,
+      payload: {
+        sampleUuid: mockUuid1,
+        fileName,
+        fileDiff: mockFile,
+        lastModified: 'newLastModified',
+      },
+    });
+
+    expect(newState).toEqual(initialState);
+  });
 });

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

@@ -234,6 +234,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl",
   },
   {
@@ -243,6 +244,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl",
   },
   {
@@ -252,6 +254,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl",
   },
 ]
@@ -401,6 +404,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl",
   },
   {
@@ -410,6 +414,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl",
   },
   {
@@ -419,6 +424,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl",
   },
 ]

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

@@ -9,6 +9,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl1",
   },
   {
@@ -18,6 +19,7 @@ exports[`processUpload Uploads and updates redux correctly when there are no err
     },
     "method": "put",
     "onUploadProgress": [Function],
+    "signal": AbortSignal {},
     "url": "theSignedUrl2",
   },
 ]

src/components/data-processing/ConfigureEmbedding/ConfigureEmbedding.jsx

@@ -7,7 +7,7 @@ import {
 } from 'antd';
 import SelectData from 'components/plots/styling/embedding-continuous/SelectData';
 
-import { isUnisample } from 'utils/experimentPredicates';
+import { getIsUnisample } from 'utils/experimentPredicates';
 
 import CategoricalEmbeddingPlot from 'components/plots/CategoricalEmbeddingPlot';
 import ContinuousEmbeddingPlot from 'components/plots/ContinuousEmbeddingPlot';
@@ -135,11 +135,11 @@ const ConfigureEmbedding = (props) => {
     const { loading, data: plotData, error } = cellMeta[colouring];
     const modifiedConfig = {
       ...config,
-      axes:{
+      axes: {
         ...config.axes,
         yAxisText: config.axes.yAxisText || plotColouring,
-      }
-    }
+      },
+    };
     return (
       <ViolinFilterPlot
         experimentId={experimentId}
@@ -406,7 +406,7 @@ const ConfigureEmbedding = (props) => {
       );
     }
 
-    if (plotColouring === 'sample' && cellSets.accessible && isUnisample(cellSets.hierarchy)
+    if (plotColouring === 'sample' && cellSets.accessible && getIsUnisample(cellSets.hierarchy)
     ) {
       return (
         <center>

src/components/data-processing/DataIntegration/DataIntegration.jsx

@@ -1,5 +1,5 @@
 import React, {
-  useState, useEffect, useRef, useCallback,
+  useState, useEffect, useRef, useCallback, useMemo,
 } from 'react';
 import { useSelector, useDispatch } from 'react-redux';
 import {
@@ -24,7 +24,7 @@ import ElbowPlot from 'components/plots/ElbowPlot';
 import { generateDataProcessingPlotUuid } from 'utils/generateCustomPlotUuid';
 import EmptyPlot from 'components/plots/helpers/EmptyPlot';
 import PlotStyling from 'components/plots/styling/PlotStyling';
-import { isUnisample } from 'utils/experimentPredicates';
+import { getIsUnisample } from 'utils/experimentPredicates';
 import PlotLegendAlert, { MAX_LEGEND_ITEMS } from 'components/plots/helpers/PlotLegendAlert';
 import CalculationConfig from './CalculationConfig';
 
@@ -33,9 +33,14 @@ const DataIntegration = (props) => {
   const {
     experimentId, onConfigChange, stepDisabled, stepHadErrors, disableDataIntegration,
   } = props;
-  const [selectedPlot, setSelectedPlot] = useState('embedding');
-  const [plot, setPlot] = useState(null);
+
   const cellSets = useSelector(getCellSets());
+
+  const isUnisample = useMemo(() => getIsUnisample(cellSets.hierarchy));
+
+  const [selectedPlot, setSelectedPlot] = useState(isUnisample ? 'elbow' : 'embedding');
+  const [plot, setPlot] = useState(null);
+
   const filterName = 'dataIntegration';
   const configureEmbeddingFilterName = 'configureEmbedding';
 
@@ -275,7 +280,7 @@ const DataIntegration = (props) => {
       );
     }
 
-    if ((selectedPlot === 'embedding' || selectedPlot === 'frequency') && cellSets.accessible && isUnisample(cellSets.hierarchy)
+    if ((selectedPlot === 'embedding' || selectedPlot === 'frequency') && cellSets.accessible && isUnisample
     ) {
       return (
         <center>

src/redux/actions/samples/createSampleFile.js

@@ -13,6 +13,7 @@ const createSampleFile = (
   sampleId,
   type,
   fileForApiV1,
+  abortController,
 ) => async (dispatch) => {
   const updatedAt = dayjs().toISOString();
 
@@ -30,8 +31,10 @@ const createSampleFile = (
         lastModified: updatedAt,
         fileName: fileNameForApiV1[type],
         fileDiff: {
-          upload: { status: UploadStatus.UPLOADING },
           ...fileForApiV1,
+          upload: {
+            status: UploadStatus.UPLOADING, progress: 0, abortController,
+          },
         },
       },
     });

src/redux/actions/samples/createSamples.js

@@ -14,6 +14,9 @@ import { defaultSampleOptions, sampleTemplate } from 'redux/reducers/samples/ini
 import { sampleTech } from 'utils/constants';
 import UploadStatus from 'utils/upload/UploadStatus';
 
+import fileNameForApiV1 from 'utils/upload/fileNameForApiV1';
+import getFileTypeV2 from 'utils/getFileTypeV2';
+
 // If the sample name of new samples coincides with already existing
 // ones we should not create new samples,
 // just reuse their sampleIds and upload the new files
@@ -115,9 +118,13 @@ const createSamples = (
         options,
         metadata: experiment?.metadataKeys
           .reduce((acc, curr) => ({ ...acc, [curr]: METADATA_DEFAULT_VALUE }), {}) || {},
-        files: Object.values(files).reduce(((acc, curr) => (
-          { ...acc, [curr.name]: { upload: { status: UploadStatus.UPLOADING } } }
-        )), {}),
+        files: Object.values(files).reduce(((acc, curr) => {
+          const fileType = fileNameForApiV1[getFileTypeV2(curr.name, sampleTechnology)];
+
+          return (
+            { ...acc, [fileType]: { upload: { status: UploadStatus.UPLOADING } } }
+          );
+        }), {}),
       }));
 
     dispatch({

src/redux/actions/samples/deleteSamples.js

@@ -11,15 +11,11 @@ import endUserMessages from 'utils/endUserMessages';
 import fetchAPI from 'utils/http/fetchAPI';
 import handleError from 'utils/http/handleError';
 
-const cancelUploads = async (files) => {
-  const promises = Object.values(files).map(({ upload }) => {
-    if (upload?.amplifyPromise) {
-      // return Storage.cancel(upload.amplifyPromise);
-    }
-    return Promise.resolve();
+const cancelUploads = (files) => {
+  Object.values(files).forEach((file) => {
+    // eslint-disable-next-line no-unused-expressions
+    file.upload?.abortController?.abort();
   });
-
-  return Promise.all(promises);
 };
 
 const deleteSamples = (
@@ -34,7 +30,7 @@ const deleteSamples = (
       acc[samples[sampleUuid].experimentId] = [];
     }
 
-    await cancelUploads(files);
+    cancelUploads(files);
 
     return {
       ...acc,

src/redux/reducers/samples/samplesFileUpdate.js

@@ -5,6 +5,12 @@ const samplesFileUpdate = (state, action) => {
     sampleUuid, fileName, fileDiff, lastModified,
   } = action.payload;
 
+  // There's a possible race condition where a file update can reach this place
+  // after a sample is deleted and there's a crash. This check is in place to avoid that error.
+  if (_.isNil(state[sampleUuid])) {
+    return state;
+  }
+
   const oldFile = state[sampleUuid].files?.[fileName];
   let newFile = fileDiff;
 

src/utils/experimentPredicates.js

@@ -1,4 +1,4 @@
-const isUnisample = (hierarchy) => hierarchy.find((rootNode) => rootNode.key === 'sample')?.children?.length === 1;
+const getIsUnisample = (hierarchy) => hierarchy.find((rootNode) => rootNode.key === 'sample')?.children?.length === 1;
 
 // eslint-disable-next-line import/prefer-default-export
-export { isUnisample };
+export { getIsUnisample };

src/utils/upload/processMultipartUpload.js

@@ -3,12 +3,15 @@ import axios from 'axios';
 const FILE_CHUNK_SIZE = 10000000;
 const MAX_RETRIES = 2;
 
-const putPartInS3 = async (blob, signedUrl, onUploadProgress, currentRetry = 0) => {
+const putPartInS3 = async (
+  blob, signedUrl, onUploadProgress, currentRetry = 0, abortController = null,
+) => {
   try {
     return await axios.request({
       method: 'put',
       data: blob,
       url: signedUrl,
+      signal: abortController.signal,
       headers: {
         'Content-Type': 'application/octet-stream',
       },
@@ -23,7 +26,9 @@ const putPartInS3 = async (blob, signedUrl, onUploadProgress, currentRetry = 0)
   }
 };
 
-const processMultipartUpload = async (file, signedUrls, createOnUploadProgressForPart) => {
+const processMultipartUpload = async (
+  file, signedUrls, createOnUploadProgressForPart, abortController,
+) => {
   const promises = [];
 
   signedUrls.forEach((signedUrl, index) => {
@@ -33,7 +38,14 @@ const processMultipartUpload = async (file, signedUrls, createOnUploadProgressFo
       ? file.fileObject.slice(start, end)
       : file.fileObject.slice(start);
 
-    const req = putPartInS3(blob, signedUrl, createOnUploadProgressForPart(index));
+    const req = putPartInS3(
+      blob,
+      signedUrl,
+      createOnUploadProgressForPart(index),
+      0,
+      abortController,
+    );
+
     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 = () => { },
+  file, uploadUrlParams, type, onStatusUpdate = () => { }, abortController = null,
 ) => {
   let parts = null;
   const { signedUrls, uploadId, fileId } = uploadUrlParams;
@@ -34,7 +34,9 @@ const prepareAndUploadFileToS3 = async (
     onStatusUpdate(UploadStatus.UPLOADING, percentProgress);
   };
   try {
-    parts = await processMultipartUpload(file, signedUrls, createOnUploadProgressForPart);
+    parts = await processMultipartUpload(
+      file, signedUrls, createOnUploadProgressForPart, abortController,
+    );
   } catch (e) {
     onStatusUpdate(UploadStatus.UPLOAD_ERROR);
     return;
@@ -64,6 +66,8 @@ const prepareAndUploadFileToS3 = async (
 const createAndUploadSampleFile = async (file, experimentId, sampleId, dispatch, selectedTech) => {
   const fileType = getFileTypeV2(file.name, selectedTech);
 
+  const abortController = new AbortController();
+
   let sampleFileId;
 
   try {
@@ -73,6 +77,7 @@ const createAndUploadSampleFile = async (file, experimentId, sampleId, dispatch,
         sampleId,
         fileType,
         file,
+        abortController,
       ),
     );
   } catch (e) {
@@ -114,8 +119,7 @@ const createAndUploadSampleFile = async (file, experimentId, sampleId, dispatch,
     );
 
     const uploadUrlParams = { signedUrls, uploadId, fileId: sampleFileId };
-
-    await prepareAndUploadFileToS3(file, uploadUrlParams, 'sample', updateSampleFileUploadProgress);
+    await prepareAndUploadFileToS3(file, uploadUrlParams, 'sample', updateSampleFileUploadProgress, abortController);
   } catch (e) {
     dispatch(updateSampleFileUpload(
       experimentId, sampleId, fileType, UploadStatus.UPLOAD_ERROR,