Merge branch 'master' into cache-disable

src/__test__/components/data-management/__snapshots__/DownloadDataButton.test.jsx.snap

@@ -22,6 +22,7 @@ exports[`DownloadDataButton Downloads processed matrix properly 1`] = `
   [
     "testae48e318dab9a1bd0bexperiment-0",
     {
+      "embeddingMethod": "umap",
       "name": "DownloadAnnotSeuratObject",
     },
     [Function],

src/__test__/components/data-processing/cellsize-distribution/CellSizeDistribution.test.jsx

@@ -10,6 +10,7 @@ import { initialPlotConfigStates } from 'redux/reducers/componentConfig/initialS
 import { generateDataProcessingPlotUuid } from 'utils/generateCustomPlotUuid';
 import CellSizeDistribution from 'components/data-processing/CellSizeDistribution/CellSizeDistribution';
 import CalculationConfig from 'components/data-processing/CellSizeDistribution/CalculationConfig';
+import SliderWithInput from 'components/SliderWithInput';
 import generateExperimentSettingsMock from '../../../test-utils/experimentSettings.mock';
 
 import filterStatisticsMock from '../../../test-utils/plotData.mock';
@@ -147,4 +148,31 @@ describe('CellSizeDistribution', () => {
     expect(plots.length).toEqual(3);
     expect(tables.length).toEqual(1);
   });
+  it('Disables bin step slider when plot type is knee plot', () => {
+    const modifiedWithData = {
+      ...withData,
+      componentConfig: {
+        ...withData.componentConfig,
+        plotType: 'kneePlot',
+      },
+    };
+
+    const store = mockStore(modifiedWithData);
+
+    const component = mount(
+      <Provider store={store}>
+        <CellSizeDistribution
+          experimentId={experimentId}
+          sampleId={sampleId}
+          sampleIds={sampleIds}
+          onConfigChange={() => { }}
+        />
+      </Provider>,
+    );
+
+    const page = component.find(CellSizeDistribution).at(0);
+    const calculationConfig = page.find(CalculationConfig);
+    const sliderWithInput = calculationConfig.find(SliderWithInput);
+    expect(sliderWithInput.props().disabled).toBe(true);
+  });
 });

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/CellSizeDistribution/CalculationConfig.jsx

@@ -16,7 +16,7 @@ const MIN_CELL_SIZE_PLACEHOLDER = 10800;
 
 const CellSizeDistributionConfig = (props) => {
   const {
-    config, disabled, updateSettings, highestUmi,
+    config, disabled, updateSettings, highestUmi, plotType,
   } = props;
 
   const withinRange = (cellSize) => Math.max(Math.min(cellSize, highestUmi), 0);
@@ -54,7 +54,7 @@ const CellSizeDistributionConfig = (props) => {
           onUpdate={(value) => {
             updateSettings({ binStep: value });
           }}
-          disabled={disabled}
+          disabled={disabled || plotType === 'kneePlot'}
         />
       </Form.Item>
     </>
@@ -65,12 +65,14 @@ CellSizeDistributionConfig.defaultProps = {
   config: {},
   disabled: false,
   highestUmi: null,
+  plotType: null,
 };
 CellSizeDistributionConfig.propTypes = {
   updateSettings: PropTypes.func,
   config: PropTypes.object,
   disabled: PropTypes.bool,
   highestUmi: PropTypes.number,
+  plotType: PropTypes.string,
 };
 
 export default CellSizeDistributionConfig;

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/extraActionCreators/downloadProcessedMatrix.js

@@ -24,6 +24,7 @@ const downloadProcessedMatrix = (experimentId) => async (dispatch, getState) =>
     // the embeddingETag is added by the API to this body
     const body = {
       name: taskName,
+      embeddingMethod,
     };
 
     const timeout = getTimeoutForWorkerTask(getState(), taskName);

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,