From 03050a55703b345c60e0551f12f7ec6df51a6cfe Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Mon, 16 Sep 2024 14:13:43 -0700
Subject: [PATCH 1/7] init sce upload; rename seurat pipeline to obj2s

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 .../DownloadDataButton.test.jsx               |  2 +-
 .../LaunchAnalysisButton.test.jsx             |  8 +--
 .../utils/experimentUpdatesHandler.test.js    | 14 ++---
 src/components/ContentWrapper.jsx             | 52 +++++++++----------
 src/components/GEM2SLoadingScreen.jsx         |  8 +--
 .../SubsetCellSetsOperation.jsx               |  4 +-
 .../data-management/FileUploadModal.jsx       | 21 ++++----
 .../data-management/LaunchAnalysisButton.jsx  | 12 ++---
 .../data-management/SamplesTable.jsx          |  6 +--
 .../metadata/AddMetadataButton.jsx            |  4 +-
 src/redux/actions/pipeline/index.js           |  4 +-
 .../pipeline/{runSeurat.js => runObj2s.js}    |  4 +-
 src/utils/constants.js                        |  4 ++
 .../calculatePipelinesRerunStatus.js          |  8 +--
 src/utils/endUserMessages.jsx                 |  8 +--
 src/utils/experimentUpdatesHandler.js         |  8 +--
 .../downloadProcessedMatrix.js                |  8 +--
 src/utils/sampleFileType.js                   |  4 +-
 src/utils/upload/fileInspector.js             |  4 +-
 src/utils/upload/fileUploadUtils.js           | 31 +++++++++++
 src/utils/upload/sampleValidators.js          |  5 +-
 src/utils/upload/validateObj2s.js             |  5 ++
 src/utils/upload/validateSeurat.js            |  5 --
 23 files changed, 134 insertions(+), 95 deletions(-)
 rename src/redux/actions/pipeline/{runSeurat.js => runObj2s.js} (89%)
 create mode 100644 src/utils/upload/validateObj2s.js
 delete mode 100644 src/utils/upload/validateSeurat.js

diff --git a/src/__test__/components/data-management/DownloadDataButton.test.jsx b/src/__test__/components/data-management/DownloadDataButton.test.jsx
index e82f0f6966..69125cfda4 100644
--- a/src/__test__/components/data-management/DownloadDataButton.test.jsx
+++ b/src/__test__/components/data-management/DownloadDataButton.test.jsx
@@ -230,7 +230,7 @@ describe('DownloadDataButton', () => {
     });
 
     expect(pushNotificationMessage).toHaveBeenCalledTimes(1);
-    expect(pushNotificationMessage).toHaveBeenCalledWith('error', endUserMessages.ERROR_DOWNLOADING_SEURAT_OBJECT);
+    expect(pushNotificationMessage).toHaveBeenCalledWith('error', endUserMessages.ERROR_DOWNLOADING_OBJ2S);
   });
 
   it('Has options disabled if backend status is still loading', async () => {
diff --git a/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx b/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
index 5f417900e2..2f07e00238 100644
--- a/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
+++ b/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
@@ -8,7 +8,7 @@ import { act } from 'react-dom/test-utils';
 import {
   screen, render, waitFor, fireEvent,
 } from '@testing-library/react';
-import { runGem2s, runSeurat } from 'redux/actions/pipeline';
+import { runGem2s, runObj2s } from 'redux/actions/pipeline';
 
 import PipelineStatus from 'utils/pipelineStatusValues';
 import { sampleTech } from 'utils/constants';
@@ -25,7 +25,7 @@ import '__test__/test-utils/setupTests';
 jest.mock('redux/actions/experimentSettings/updateExperimentInfo', () => jest.fn().mockReturnValue({ type: 'UPDATE_EXPERIMENT_INFO' }));
 jest.mock('redux/actions/pipeline', () => ({
   runGem2s: jest.fn().mockReturnValue({ type: 'RUN_GEM2S' }),
-  runSeurat: jest.fn().mockReturnValue({ type: 'RUN_SEURAT' }),
+  runObj2s: jest.fn().mockReturnValue({ type: 'RUN_OBJ2S' }),
 }));
 
 const mockNavigateTo = jest.fn();
@@ -495,7 +495,7 @@ describe('LaunchAnalysisButton', () => {
     expect(mockNavigateTo).toHaveBeenCalled();
   });
 
-  it('Does dispatch a request to runSeurat for an unprocessed experiment', async () => {
+  it('Does dispatch a request to runObj2s for an unprocessed experiment', async () => {
     calculateGem2sRerunStatus.mockReturnValue(rerunState);
     calculateQCRerunStatus.mockReturnValue(notRerunState);
 
@@ -529,6 +529,6 @@ describe('LaunchAnalysisButton', () => {
     fireEvent.click(screen.getByText('Yes'));
 
     expect(runGem2s).not.toHaveBeenCalled();
-    expect(runSeurat).toHaveBeenCalled();
+    expect(runObj2s).toHaveBeenCalled();
   });
 });
diff --git a/src/__test__/utils/experimentUpdatesHandler.test.js b/src/__test__/utils/experimentUpdatesHandler.test.js
index 5abc168a93..698cd1f317 100644
--- a/src/__test__/utils/experimentUpdatesHandler.test.js
+++ b/src/__test__/utils/experimentUpdatesHandler.test.js
@@ -94,8 +94,8 @@ const mockWorkResponseUpdate = {
   },
 };
 
-const mockSeuratUpdate = {
-  type: updateTypes.SEURAT,
+const mockObj2sUpdate = {
+  type: updateTypes.OBJ2S,
   item: {
     processingConfig: {
       mockProcessingConfig: 'mockProcessingConfig',
@@ -131,8 +131,8 @@ describe('ExperimentUpdatesHandler', () => {
     expect(pushNotificationMessage).not.toHaveBeenCalled();
   });
 
-  it('Triggers properly for SEURAT updates ', () => {
-    const mockUpdate = mockSeuratUpdate;
+  it('Triggers properly for OBJ2S updates ', () => {
+    const mockUpdate = mockObj2sUpdate;
 
     triggerExperimentUpdate(mockUpdate);
 
@@ -145,8 +145,8 @@ describe('ExperimentUpdatesHandler', () => {
     expect(pushNotificationMessage).not.toHaveBeenCalled();
   });
 
-  it('Triggers properly for SEURAT updates ', () => {
-    const mockUpdate = mockSeuratUpdate;
+  it('Triggers properly for OBJ2S updates ', () => {
+    const mockUpdate = mockObj2sUpdate;
 
     triggerExperimentUpdate(mockUpdate);
 
@@ -160,7 +160,7 @@ describe('ExperimentUpdatesHandler', () => {
 
   it('Loads cell sets if Seurat pipeline completes ', () => {
     const mockUpdate = {
-      ...mockSeuratUpdate,
+      ...mockObj2sUpdate,
       status: {
         seurat: {
           status: 'SUCCEEDED',
diff --git a/src/components/ContentWrapper.jsx b/src/components/ContentWrapper.jsx
index e6423d6ad0..de4bd62f5c 100644
--- a/src/components/ContentWrapper.jsx
+++ b/src/components/ContentWrapper.jsx
@@ -33,7 +33,7 @@ import { loadUser } from 'redux/actions/user';
 import { loadBackendStatus } from 'redux/actions/backendStatus';
 
 import { isBrowser, privacyPolicyIsNotAccepted } from 'utils/deploymentInfo';
-import { modules } from 'utils/constants';
+import { modules, obj2sTechs } from 'utils/constants';
 import { useAppRouter } from 'utils/AppRouteProvider';
 import experimentUpdatesHandler from 'utils/experimentUpdatesHandler';
 import integrationTestConstants from 'utils/integrationTestConstants';
@@ -105,15 +105,15 @@ const ContentWrapper = (props) => {
   const gem2sRunning = gem2sStatusKey === 'RUNNING';
   const gem2sRunningError = backendErrors.includes(gem2sStatusKey);
   const completedGem2sSteps = backendStatus?.gem2s?.completedSteps;
-  const seuratStatusKey = backendStatus?.seurat?.status;
+  const obj2sStatusKey = backendStatus?.seurat?.status;
 
-  const isSeurat = seuratStatusKey && selectedTechnology === 'seurat';
+  const isObj2s = obj2sStatusKey && obj2sTechs.includes(selectedTechnology);
 
   const [pipelinesRerunStatus, setPipelinesRerunStatus] = useState(null);
-  const seuratRunning = seuratStatusKey === 'RUNNING' && isSeurat;
-  const seuratRunningError = backendErrors.includes(seuratStatusKey) && isSeurat;
-  const completedSeuratSteps = backendStatus?.seurat?.completedSteps;
-  const seuratComplete = (seuratStatusKey === pipelineStatusValues.SUCCEEDED) && isSeurat;
+  const obj2sRunning = obj2sStatusKey === 'RUNNING' && isObj2s;
+  const obj2sRunningError = backendErrors.includes(obj2sStatusKey) && isObj2s;
+  const completedObj2sSteps = backendStatus?.seurat?.completedSteps;
+  const obj2sComplete = (obj2sStatusKey === pipelineStatusValues.SUCCEEDED) && isObj2s;
   const waitingForQcToLaunch = gem2sStatusKey === pipelineStatusValues.SUCCEEDED
     && qcStatusKey === pipelineStatusValues.NOT_CREATED;
   // This is used to prevent a race condition where the page would start loading immediately
@@ -154,7 +154,7 @@ const ContentWrapper = (props) => {
     if (!experiment || !backendStatus) return;
 
     // The value of backend status is null for new experiments that have never run
-    const setupPipeline = isSeurat ? 'seurat' : 'gem2s';
+    const setupPipeline = isObj2s ? 'seurat' : 'gem2s';
     const {
       pipeline: qcBackendStatus, [setupPipeline]: setupBackendStatus,
     } = backendStatus ?? {};
@@ -169,7 +169,7 @@ const ContentWrapper = (props) => {
         setupBackendStatus,
         qcBackendStatus,
         experiment,
-        isSeurat,
+        isObj2s,
       ),
     );
   }, [backendStatus, experiment, samples]);
@@ -187,16 +187,16 @@ const ContentWrapper = (props) => {
   });
 
   const gem2sNotCreated = checkEveryIsValue(
-    [gem2sStatusKey, seuratStatusKey], pipelineStatusValues.NOT_CREATED,
+    [gem2sStatusKey, obj2sStatusKey], pipelineStatusValues.NOT_CREATED,
   );
 
-  const getSeuratStatus = () => {
-    if (seuratRunningError) {
+  const getObj2sStatus = () => {
+    if (obj2sRunningError) {
       const errorMessage = pipelineErrorUserMessages[backendStatus?.seurat?.error?.error];
-      return getStatusObject('seurat', 'error', errorMessage);
+      return getStatusObject('obj2s', 'error', errorMessage);
     }
-    if (seuratRunning) {
-      return getStatusObject('seurat', 'running', null, completedSeuratSteps);
+    if (obj2sRunning) {
+      return getStatusObject('obj2s', 'running', null, completedObj2sSteps);
     }
     return null;
   };
@@ -225,8 +225,8 @@ const ContentWrapper = (props) => {
   };
 
   const getCurrentStatusScreen = () => {
-    if (isSeurat) {
-      return getSeuratStatus();
+    if (isObj2s) {
+      return getObj2sStatus();
     }
     return getGem2sStatus() || getQcStatus();
   };
@@ -309,7 +309,7 @@ const ContentWrapper = (props) => {
       name: 'Data Management',
       disableIfNoExperiment: false,
       disabledByPipelineStatus: true,
-      disabledIfSeuratComplete: false,
+      disabledIfObj2sComplete: false,
     },
     {
       module: modules.DATA_PROCESSING,
@@ -317,7 +317,7 @@ const ContentWrapper = (props) => {
       name: 'Data Processing',
       disableIfNoExperiment: true,
       disabledByPipelineStatus: false,
-      disabledIfSeuratComplete: true,
+      disabledIfObj2sComplete: true,
     },
     {
       module: modules.DATA_EXPLORATION,
@@ -325,7 +325,7 @@ const ContentWrapper = (props) => {
       name: 'Data Exploration',
       disableIfNoExperiment: true,
       disabledByPipelineStatus: true,
-      disabledIfSeuratComplete: false,
+      disabledIfObj2sComplete: false,
     },
     {
       module: modules.PLOTS_AND_TABLES,
@@ -333,7 +333,7 @@ const ContentWrapper = (props) => {
       name: 'Plots and Tables',
       disableIfNoExperiment: true,
       disabledByPipelineStatus: true,
-      disabledIfSeuratComplete: false,
+      disabledIfObj2sComplete: false,
     },
   ];
 
@@ -363,7 +363,7 @@ const ContentWrapper = (props) => {
         );
       }
 
-      if (seuratComplete && currentModule === modules.DATA_PROCESSING) {
+      if (obj2sComplete && currentModule === modules.DATA_PROCESSING) {
         navigateTo(modules.DATA_EXPLORATION, { experimentId: routeExperimentId });
         return <></>;
       }
@@ -377,7 +377,7 @@ const ContentWrapper = (props) => {
   };
 
   const menuItemRender = ({
-    module, icon, name, disableIfNoExperiment, disabledByPipelineStatus, disabledIfSeuratComplete,
+    module, icon, name, disableIfNoExperiment, disabledByPipelineStatus, disabledIfObj2sComplete,
   }) => {
     const needRerunPipeline = pipelinesRerunStatus === null || pipelinesRerunStatus.rerun;
 
@@ -387,7 +387,7 @@ const ContentWrapper = (props) => {
     const pipelineStatusDisable = disabledByPipelineStatus && (
       backendError || gem2sRunning || gem2sRunningError
       || waitingForQcToLaunch || qcRunning || qcRunningError
-      || seuratRunning || seuratRunningError
+      || obj2sRunning || obj2sRunningError
     );
 
     const {
@@ -398,14 +398,14 @@ const ContentWrapper = (props) => {
     const nonExperimentModule = ![DATA_EXPLORATION,
       DATA_MANAGEMENT, DATA_PROCESSING, PLOTS_AND_TABLES]
       .includes(currentModule) && disableIfNoExperiment;
-    const seuratCompleteDisable = disabledIfSeuratComplete && seuratComplete;
+    const obj2sCompleteDisable = disabledIfObj2sComplete && obj2sComplete;
 
     return {
       key: module,
       icon,
       label: name,
       disabled: notProcessedExperimentDisable || pipelineStatusDisable
-      || seuratCompleteDisable || nonExperimentModule,
+      || obj2sCompleteDisable || nonExperimentModule,
       onClick: () => navigateTo(
         module,
         { experimentId: currentExperimentId },
diff --git a/src/components/GEM2SLoadingScreen.jsx b/src/components/GEM2SLoadingScreen.jsx
index dc509b18aa..6ea23c3d4b 100644
--- a/src/components/GEM2SLoadingScreen.jsx
+++ b/src/components/GEM2SLoadingScreen.jsx
@@ -20,9 +20,9 @@ const pipelineStepsInfoByType = {
     'Uploading completed data',
   ],
 
-  seurat: [
-    'Downloading RDS file',
-    'Processing Seurat object',
+  obj2s: [
+    'Downloading project data',
+    'Processing object',
     'Uploading completed data',
   ],
 };
@@ -168,7 +168,7 @@ const GEM2SLoadingScreen = (props) => {
 
 GEM2SLoadingScreen.propTypes = {
   pipelineStatus: PropTypes.oneOf(['error', 'running', 'toBeRun', 'subsetting']).isRequired,
-  pipelineType: PropTypes.oneOf(['gem2s', 'seurat']).isRequired,
+  pipelineType: PropTypes.oneOf(['gem2s', 'obj2s']).isRequired,
   completedSteps: PropTypes.array,
   experimentId: PropTypes.string,
   experimentName: PropTypes.string,
diff --git a/src/components/data-exploration/cell-sets-tool/SubsetCellSetsOperation.jsx b/src/components/data-exploration/cell-sets-tool/SubsetCellSetsOperation.jsx
index 9659e726b6..63c0ebf707 100644
--- a/src/components/data-exploration/cell-sets-tool/SubsetCellSetsOperation.jsx
+++ b/src/components/data-exploration/cell-sets-tool/SubsetCellSetsOperation.jsx
@@ -7,7 +7,7 @@ import { Tooltip, Button } from 'antd';
 import { PieChartOutlined } from '@ant-design/icons';
 
 import SubsetCellSetsModal from 'components/data-exploration/cell-sets-tool/SubsetCellSetsModal';
-import { sampleTech } from 'utils/constants';
+import { obj2sTechs } from 'utils/constants';
 
 const SubsetCellSetsOperation = (props) => {
   const { onCreate } = props;
@@ -23,7 +23,7 @@ const SubsetCellSetsOperation = (props) => {
       <Tooltip placement='top' title='Subset selected cell sets to a new project.'>
         <Button
           type='dashed'
-          disabled={experimentType === sampleTech.SEURAT}
+          disabled={obj2sTechs.includes(experimentType)}
           aria-label='Create new experiment from selected cellsets'
           size='small'
           icon={<PieChartOutlined />}
diff --git a/src/components/data-management/FileUploadModal.jsx b/src/components/data-management/FileUploadModal.jsx
index 00328b3102..00cc415e24 100644
--- a/src/components/data-management/FileUploadModal.jsx
+++ b/src/components/data-management/FileUploadModal.jsx
@@ -24,7 +24,7 @@ import config from 'config';
 
 import Expandable from 'components/Expandable';
 
-import { sampleTech } from 'utils/constants';
+import { sampleTech, obj2sTechs } from 'utils/constants';
 import fileUploadUtils, { techNamesToDisplay } from 'utils/upload/fileUploadUtils';
 import handleError from 'utils/http/handleError';
 import { fileObjectToFileRecord } from 'utils/upload/processSampleUpload';
@@ -36,11 +36,12 @@ const { Text, Title, Paragraph } = Typography;
 const { Option } = Select;
 
 // allow at most 15 GiB .rds object uploads
-const SEURAT_MAX_FILE_SIZE = 15 * 1024 * 1024 * 1024;
+const OBJ2S_MAX_FILE_SIZE = 15 * 1024 * 1024 * 1024;
 
 const extraHelpText = {
   [sampleTech['10X']]: () => <></>,
   [sampleTech.SEURAT]: () => <></>,
+  [sampleTech.SINGLE_CELL_EXPERIMENT]: () => <></>,
   [sampleTech.H5]: () => <></>,
   [sampleTech.RHAPSODY]: () => (
     <Paragraph>
@@ -87,30 +88,30 @@ const FileUploadModal = (props) => {
     const filteredFiles = acceptedFiles
       .filter((file) => !file.name.startsWith('.') && !file.name.startsWith('__MACOSX'));
 
-    if (selectedTech === sampleTech.SEURAT) {
-      // TODO1 this needs to be further refactored before it is moved into
+    if (obj2sTechs.includes(selectedTech)) {
+      // TODO this needs to be further refactored before it is moved into
       // fileUploadUtils as a filterFiles call, right now it's a bit unnecessarily complicated
       const newFiles = await Promise.all(filteredFiles.map((file) => (
         fileObjectToFileRecord(file, selectedTech)
       )));
 
       if (previouslyUploadedSamples.length) {
-        handleError('error', endUserMessages.ERROR_SEURAT_EXISTING_FILE);
+        handleError('error', endUserMessages.ERROR_OBJ2S_EXISTING_FILE);
         return;
       }
 
       const allFiles = [...files.valid, ...newFiles];
       if (allFiles.length > 1) {
-        handleError('error', endUserMessages.ERROR_SEURAT_MULTIPLE_FILES);
+        handleError('error', endUserMessages.ERROR_OBJ2S_MULTIPLE_FILES);
       }
 
-      const seuratFile = allFiles[0];
-      if (seuratFile.size > SEURAT_MAX_FILE_SIZE) {
-        handleError('error', endUserMessages.ERROR_SEURAT_MAX_FILE_SIZE);
+      const obj2sFile = allFiles[0];
+      if (obj2sFile.size > OBJ2S_MAX_FILE_SIZE) {
+        handleError('error', endUserMessages.ERROR_OBJ2S_MAX_FILE_SIZE);
         return;
       }
 
-      setFiles({ valid: [seuratFile], invalid: [] });
+      setFiles({ valid: [obj2sFile], invalid: [] });
     } else {
       const {
         valid: newFiles,
diff --git a/src/components/data-management/LaunchAnalysisButton.jsx b/src/components/data-management/LaunchAnalysisButton.jsx
index 1afaeb93db..b4dbe69900 100644
--- a/src/components/data-management/LaunchAnalysisButton.jsx
+++ b/src/components/data-management/LaunchAnalysisButton.jsx
@@ -5,7 +5,7 @@ import {
 } from 'antd';
 import _ from 'lodash';
 
-import { modules, sampleTech } from 'utils/constants';
+import { modules, sampleTech, obj2sTechs } from 'utils/constants';
 
 import UploadStatus from 'utils/upload/UploadStatus';
 import integrationTestConstants from 'utils/integrationTestConstants';
@@ -27,7 +27,7 @@ const LaunchAnalysisButton = () => {
   const { activeExperimentId } = experiments.meta;
   const activeExperiment = experiments[activeExperimentId];
   const selectedTech = samples[activeExperiment?.sampleIds[0]]?.type;
-  const isTechSeurat = selectedTech === sampleTech.SEURAT;
+  const isObj2s = obj2sTechs.includes(selectedTech);
 
   const [pipelinesRerunStatus, setPipelinesRerunStatus] = useState({
     runPipeline: null, rerun: true, reasons: [], complete: false,
@@ -40,7 +40,7 @@ const LaunchAnalysisButton = () => {
     }
 
     if (shouldNavigate) {
-      const moduleName = isTechSeurat && pipelinesRerunStatus.complete
+      const moduleName = isObj2s && pipelinesRerunStatus.complete
         ? modules.DATA_EXPLORATION : modules.DATA_PROCESSING;
       navigateTo(moduleName, { experimentId: activeExperimentId });
     }
@@ -48,7 +48,7 @@ const LaunchAnalysisButton = () => {
 
   useEffect(() => {
     // The value of backend status is null for new experiments that have never run
-    const setupPipeline = isTechSeurat ? 'seurat' : 'gem2s';
+    const setupPipeline = isObj2s ? 'seurat' : 'gem2s';
     const {
       pipeline: qcBackendStatus, [setupPipeline]: setupBackendStatus,
     } = backendStatus[activeExperimentId]?.status ?? {};
@@ -63,7 +63,7 @@ const LaunchAnalysisButton = () => {
         setupBackendStatus,
         qcBackendStatus,
         activeExperiment,
-        isTechSeurat,
+        isObj2s,
       ),
     );
   }, [backendStatus, activeExperimentId, samples, activeExperiment]);
@@ -167,7 +167,7 @@ const LaunchAnalysisButton = () => {
 
     if (pipelinesRerunStatus.rerun) {
       buttonText = 'Process project';
-    } else if (isTechSeurat && pipelinesRerunStatus.complete) {
+    } else if (isObj2s && pipelinesRerunStatus.complete) {
       buttonText = 'Go to Data Exploration';
     } else {
       buttonText = 'Go to Data Processing';
diff --git a/src/components/data-management/SamplesTable.jsx b/src/components/data-management/SamplesTable.jsx
index 30815653d8..b0843b76a7 100644
--- a/src/components/data-management/SamplesTable.jsx
+++ b/src/components/data-management/SamplesTable.jsx
@@ -37,7 +37,7 @@ import { metadataNameToKey, metadataKeyToName, temporaryMetadataKey } from 'util
 import integrationTestConstants from 'utils/integrationTestConstants';
 import useConditionalEffect from 'utils/customHooks/useConditionalEffect';
 import fileUploadUtils from 'utils/upload/fileUploadUtils';
-import { sampleTech } from 'utils/constants';
+import { obj2sTechs } from 'utils/constants';
 import { fileTypeToDisplay } from 'utils/sampleFileType';
 
 const { Text } = Typography;
@@ -79,7 +79,7 @@ const SamplesTable = forwardRef((props, ref) => {
           title: <center>{fileTypeToDisplay[requiredFile]}</center>,
           key: requiredFile,
           dataIndex: requiredFile,
-          width: 170,
+          width: 210,
           onCell: () => ({ style: { margin: '0px', padding: '0px' } }),
           render: (tableCellData) => tableCellData && (
             <UploadCell
@@ -104,7 +104,7 @@ const SamplesTable = forwardRef((props, ref) => {
         className: `${integrationTestConstants.classes.SAMPLE_CELL}`,
         index: 1,
         key: 'sample',
-        title: selectedTech === sampleTech.SEURAT ? 'File' : 'Sample',
+        title: obj2sTechs.includes(selectedTech) ? 'File' : 'Sample',
         dataIndex: 'name',
         fixed: 'left',
         render: (text, record, indx) => (
diff --git a/src/components/data-management/metadata/AddMetadataButton.jsx b/src/components/data-management/metadata/AddMetadataButton.jsx
index 330e2e8f54..37834c327b 100644
--- a/src/components/data-management/metadata/AddMetadataButton.jsx
+++ b/src/components/data-management/metadata/AddMetadataButton.jsx
@@ -8,7 +8,7 @@ import PropTypes from 'prop-types';
 import { useSelector, useDispatch } from 'react-redux';
 
 import uploadMetadataFile from 'redux/actions/experiments/uploadMetadataFile';
-import { sampleTech } from 'utils/constants';
+import { obj2sTechs } from 'utils/constants';
 import {
   createCellLevelMetadata,
   updateCellLevelMetadataFileUpload,
@@ -109,7 +109,7 @@ const AddMetadataButton = ({ samplesTableRef }) => {
         disabled={
           activeExperiment.sampleIds?.length === 0
           || isSubsetted
-          || selectedTech === sampleTech.SEURAT
+          || obj2sTechs.includes(selectedTech)
         }
       >
         <Button>
diff --git a/src/redux/actions/pipeline/index.js b/src/redux/actions/pipeline/index.js
index 9599cccf6b..7e134e5bd0 100644
--- a/src/redux/actions/pipeline/index.js
+++ b/src/redux/actions/pipeline/index.js
@@ -1,13 +1,13 @@
 import runQC from './runQC';
 import runGem2s from './runGem2s';
 import runSubsetExperiment from './runSubsetExperiment';
-import runSeurat from './runSeurat';
+import runObj2s from './runObj2s';
 import retry from './retry';
 
 export {
   runQC,
   runGem2s,
   runSubsetExperiment,
-  runSeurat,
+  runObj2s,
   retry,
 };
diff --git a/src/redux/actions/pipeline/runSeurat.js b/src/redux/actions/pipeline/runObj2s.js
similarity index 89%
rename from src/redux/actions/pipeline/runSeurat.js
rename to src/redux/actions/pipeline/runObj2s.js
index da6906eab3..3ad03f4a7b 100644
--- a/src/redux/actions/pipeline/runSeurat.js
+++ b/src/redux/actions/pipeline/runObj2s.js
@@ -3,7 +3,7 @@ import handleError from 'utils/http/handleError';
 import endUserMessages from 'utils/endUserMessages';
 import loadBackendStatus from 'redux/actions/backendStatus/loadBackendStatus';
 
-const runSeurat = (experimentId) => async (dispatch) => {
+const runObj2s = (experimentId) => async (dispatch) => {
   try {
     await fetchAPI(
       `/v2/experiments/${experimentId}/seurat`,
@@ -29,4 +29,4 @@ const runSeurat = (experimentId) => async (dispatch) => {
   }
 };
 
-export default runSeurat;
+export default runObj2s;
diff --git a/src/utils/constants.js b/src/utils/constants.js
index a5c8d7bf4f..2a3aa84bf6 100644
--- a/src/utils/constants.js
+++ b/src/utils/constants.js
@@ -19,10 +19,13 @@ const sampleTech = {
   '10X': '10x',
   RHAPSODY: 'rhapsody',
   SEURAT: 'seurat',
+  SINGLE_CELL_EXPERIMENT: 'single_cell_experiment',
   H5: '10x_h5',
   PARSE: 'parse',
 };
 
+const obj2sTechs = [sampleTech.SEURAT, sampleTech.SINGLE_CELL_EXPERIMENT];
+
 const plotTypes = {
   CONTINUOUS_EMBEDDING: 'embeddingContinuous',
   CATEGORICAL_EMBEDDING: 'embeddingCategorical',
@@ -82,6 +85,7 @@ export {
   api,
   modules,
   sampleTech,
+  obj2sTechs,
   plotTypes,
   plotUuids,
   plotNames,
diff --git a/src/utils/data-management/calculatePipelinesRerunStatus.js b/src/utils/data-management/calculatePipelinesRerunStatus.js
index 2b2977cb4e..ffb9872491 100644
--- a/src/utils/data-management/calculatePipelinesRerunStatus.js
+++ b/src/utils/data-management/calculatePipelinesRerunStatus.js
@@ -1,4 +1,4 @@
-import { runGem2s, runQC, runSeurat } from 'redux/actions/pipeline';
+import { runGem2s, runQC, runObj2s } from 'redux/actions/pipeline';
 import calculateGem2sRerunStatus from 'utils/data-management/calculateGem2sRerunStatus';
 import calculateQCRerunStatus from 'utils/data-management/calculateQCRerunStatus';
 
@@ -6,19 +6,19 @@ const calculatePipelinesRerunStatus = (
   gem2sBackendStatus,
   qcBackendStatus,
   activeExperiment,
-  isTechSeurat,
+  isObj2s,
 ) => {
   const gem2sRerunStatus = calculateGem2sRerunStatus(gem2sBackendStatus, activeExperiment);
   const qcRerunStatus = calculateQCRerunStatus(qcBackendStatus, gem2sBackendStatus);
 
   if (gem2sRerunStatus.rerun) {
     return {
-      runPipeline: isTechSeurat ? runSeurat : runGem2s,
+      runPipeline: isObj2s ? runObj2s : runGem2s,
       ...gem2sRerunStatus,
     };
   }
 
-  if (isTechSeurat) {
+  if (isObj2s) {
     return {
       runPipeline: null,
       rerun: false,
diff --git a/src/utils/endUserMessages.jsx b/src/utils/endUserMessages.jsx
index 01724b7836..34309a3063 100644
--- a/src/utils/endUserMessages.jsx
+++ b/src/utils/endUserMessages.jsx
@@ -29,9 +29,9 @@ export default {
   ERROR_METADATA_MULTIPLE_FILES: 'You need to upload a single file in .tsv format',
   ERROR_METADATA_WRONG_FORMAT: 'The file does not seem to be in the correct tsv key-value format.',
   ERROR_CELL_LEVEL_COLUMN: 'The .tsv file needs to contain the column "barcode"',
-  ERROR_SEURAT_MULTIPLE_FILES: 'Only a single rds file is accepted for Seurat uploads.',
-  ERROR_SEURAT_EXISTING_FILE: 'Please remove existing seurat rds file before uploading a new one.',
-  ERROR_SEURAT_MAX_FILE_SIZE: 'rds objects must be less than 15 GB.',
+  ERROR_OBJ2S_MULTIPLE_FILES: 'Only a single rds file is accepted for uploads.',
+  ERROR_OBJ2S_EXISTING_FILE: 'Please remove existing rds file before uploading a new one.',
+  ERROR_OBJ2S_MAX_FILE_SIZE: 'rds objects must be less than 15 GB.',
   ERROR_NOT_SIGNED_IN: 'You need to sign in first. Click Sign in on the top right to begin.',
   ERROR_NO_PERMISSIONS: 'You do not have permissions to perform that action.',
   ERROR_LAUNCH_PATHWAY: 'We couldn\'t launch pathway analysis',
@@ -42,7 +42,7 @@ export default {
   ERROR_SAVING_PLOT_CONFIG: 'We couldn\'t save your plot configuration.',
   ERROR_STARTING_PIPLELINE: 'We couldn\'t start working on your data.',
   ERROR_SIGN_IN: 'We couldn\'t sign you in. Please try again.',
-  ERROR_DOWNLOADING_SEURAT_OBJECT: 'We couldn\'t get the processed Seurat object.',
+  ERROR_DOWNLOADING_OBJ2S: 'We couldn\'t get the processed object.',
   FEEDBACK_ERROR: 'We couldn\'t process your feedback. Please try submitting again.',
   FEEDBACK_SUCCESSFUL: 'Your feedback has been successfully sent. Thank you!',
   REFERRAL_ERROR: 'We couldn\'t process your referral. Please try submitting again.',
diff --git a/src/utils/experimentUpdatesHandler.js b/src/utils/experimentUpdatesHandler.js
index e2b19c79e2..492dbd6153 100644
--- a/src/utils/experimentUpdatesHandler.js
+++ b/src/utils/experimentUpdatesHandler.js
@@ -12,7 +12,7 @@ import endUserMessages from 'utils/endUserMessages';
 const updateTypes = {
   QC: 'qc',
   GEM2S: 'gem2s',
-  SEURAT: 'seurat',
+  OBJ2S: 'seurat',
   WORK_RESPONSE: 'WorkResponse',
   PLOT_CONFIG_REFRESH: 'PlotConfigRefresh',
 };
@@ -36,8 +36,8 @@ const experimentUpdatesHandler = (dispatch) => (experimentId, update) => {
     case updateTypes.GEM2S: {
       return onGEM2SUpdate(update, dispatch, experimentId);
     }
-    case updateTypes.SEURAT: {
-      return onSeuratUpdate(update, dispatch, experimentId);
+    case updateTypes.OBJ2S: {
+      return onObj2sUpdate(update, dispatch, experimentId);
     }
     case updateTypes.WORK_RESPONSE: {
       return onWorkResponseUpdate(update, dispatch, experimentId);
@@ -116,7 +116,7 @@ const onPlotConfigRefresh = (update, dispatch) => {
   dispatch(replaceLoadedConfigs(update.updatedConfigs));
 };
 
-const onSeuratUpdate = (update, dispatch, experimentId) => {
+const onObj2sUpdate = (update, dispatch, experimentId) => {
   // If the pipeline finished we have a new clustering, so fetch it
   if (update.status.seurat.status === 'SUCCEEDED') {
     dispatch(loadCellSets(experimentId, true));
diff --git a/src/utils/extraActionCreators/downloadProcessedMatrix.js b/src/utils/extraActionCreators/downloadProcessedMatrix.js
index 5ce5e48d46..2460707227 100644
--- a/src/utils/extraActionCreators/downloadProcessedMatrix.js
+++ b/src/utils/extraActionCreators/downloadProcessedMatrix.js
@@ -14,21 +14,21 @@ const downloadProcessedMatrix = (experimentId) => async (dispatch, getState) =>
 
     const {
       method: embeddingMethod,
-      // embedding is saved in R object if downloading from project created by Seurat object upload
+      // embedding is saved in R object if downloading from project created by Seurat/SingleCellExperiment object upload
       useSaved,
     } = getState().experimentSettings.processing.configureEmbedding.embeddingSettings;
 
     await dispatch(loadEmbedding(experimentId, embeddingMethod, true));
 
     const taskName = 'DownloadAnnotSeuratObject';
-    const isSeurat = useSaved || false;
+    const isObj2s = useSaved || false;
 
     // the request needs the embeddingETag to merge that data with the rds
     // the embeddingETag is added by the API to this body
     const body = {
       name: taskName,
       embeddingMethod,
-      isSeurat,
+      isObj2s,
     };
 
     const timeout = getTimeoutForWorkerTask(getState(), taskName);
@@ -39,7 +39,7 @@ const downloadProcessedMatrix = (experimentId) => async (dispatch, getState) =>
 
     downloadFromUrl(writeToFileURL(data), `${experimentId}_processed_matrix.rds`);
   } catch (e) {
-    handleError(e, endUserMessages.ERROR_DOWNLOADING_SEURAT_OBJECT);
+    handleError(e, endUserMessages.ERROR_DOWNLOADING_OBJ2S);
   }
 };
 
diff --git a/src/utils/sampleFileType.js b/src/utils/sampleFileType.js
index 9b87eaf244..0ed92340bd 100644
--- a/src/utils/sampleFileType.js
+++ b/src/utils/sampleFileType.js
@@ -4,6 +4,7 @@ const sampleFileType = {
   MATRIX_10_X: 'matrix10x',
   H5_10_X: '10x_h5',
   SEURAT: 'seurat',
+  SINGLE_CELL_EXPERIMENT: 'single_cell_experiment',
   RHAPSODY: 'rhapsody',
   FEATURES_PARSE: 'featuresParse',
   BARCODES_PARSE: 'barcodesParse',
@@ -15,7 +16,8 @@ const fileTypeToDisplay = {
   [sampleFileType.FEATURES_10_X]: 'genes.tsv',
   [sampleFileType.MATRIX_10_X]: 'matrix.mtx',
   [sampleFileType.H5_10_X]: 'matrix.h5',
-  [sampleFileType.SEURAT]: 'seurat rds',
+  [sampleFileType.SEURAT]: 'Seurat RDS',
+  [sampleFileType.SINGLE_CELL_EXPERIMENT]: 'SingleCellExperiment RDS',
   [sampleFileType.FEATURES_PARSE]: 'all_genes.csv',
   [sampleFileType.BARCODES_PARSE]: 'cell_metadata.csv',
   [sampleFileType.MATRIX_PARSE]: 'count_matrix.mtx',
diff --git a/src/utils/upload/fileInspector.js b/src/utils/upload/fileInspector.js
index 17fd29c75f..64991f3a1d 100644
--- a/src/utils/upload/fileInspector.js
+++ b/src/utils/upload/fileInspector.js
@@ -1,6 +1,6 @@
 import { Gunzip } from 'fflate';
 
-import { sampleTech } from 'utils/constants';
+import { sampleTech, obj2sTechs } from 'utils/constants';
 import techOptions from 'utils/upload/fileUploadUtils';
 import readFileToBuffer from 'utils/upload/readFileToBuffer';
 
@@ -30,7 +30,7 @@ const inspectFile = async (file, technology) => {
   // Validate a file requested for upload to the platform.
   if (technology === sampleTech['10X']) {
     return inspect10XFile(file);
-  } if (technology === sampleTech.SEURAT) {
+  } if (obj2sTechs.includes(technology)) {
     // only extension is checked
     return Verdict.VALID_ZIPPED;
   } if (technology === sampleTech.RHAPSODY) {
diff --git a/src/utils/upload/fileUploadUtils.js b/src/utils/upload/fileUploadUtils.js
index 9f92c1279d..9613df5743 100644
--- a/src/utils/upload/fileUploadUtils.js
+++ b/src/utils/upload/fileUploadUtils.js
@@ -10,6 +10,7 @@ const techNamesToDisplay = {
   [sampleTech['10X']]: '10X Chromium',
   [sampleTech.RHAPSODY]: 'BD Rhapsody',
   [sampleTech.SEURAT]: 'Seurat',
+  [sampleTech.SINGLE_CELL_EXPERIMENT]: 'SingleCellExperiment',
   [sampleTech.H5]: '10X Chromium - H5',
   [sampleTech.PARSE]: 'Parse Evercode WT',
 };
@@ -141,6 +142,36 @@ const fileUploadUtils = {
     getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech.SEURAT),
     getFileSampleAndName: getFileSampleAndNameDefault,
   },
+  [sampleTech.SINGLE_CELL_EXPERIMENT]: {
+    validExtensionTypes: ['.rds'],
+    inputInfo: [
+      ['<code>scdata$samples</code>: sample assignment. If absent, treated as unisample.'],
+      ['<code>scdata[[\'RNA\']]@counts</code>: raw feature counts.'],
+      ['<code>scdata@reductions</code>: includes a <code>pca</code> reduction.'],
+      ['<code>DefaultDimReduc(scdata)</code>: includes either <code>umap</code> or <code>tsne</code> (e.g. <code>ref.umap</code> will work).'],
+      ['\uD83D\uDCA1cluster metadata in <code>scdata@meta.data</code> is auto-detected.'],
+      ['\uD83D\uDCA1sample level metadata in <code>scdata@meta.data</code> that groups samples in <code>scdata$samples</code> is auto-detected for downstream analysis.'],
+      ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'],
+    ],
+    requiredFiles: ['single_cell_experiment'],
+    fileUploadParagraphs: [
+      '<p>For your dataset, upload a single <code>*.rds</code> file with the SingleCellExperiment object (max 15GB).</p>',
+      '<p>The SingleCellExperiment object must contain the following slots and metadata:</p>',
+    ],
+    dropzoneText: 'Drag and drop *.rds file here or click to browse.',
+    // setting to null allows file upload on dropzone click
+    webkitdirectory: null,
+    isNameValid(fileName) {
+      return this.validExtensionTypes.some(
+        (validExtension) => fileName.endsWith(validExtension),
+      );
+    },
+    getCorrespondingType: () => 'single_cell_experiment',
+    // For more information on this one check the TODO1 at FileUploadModal
+    filterFiles: () => { throw new Error('Not Implemented'); },
+    getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech.SINGLE_CELL_EXPERIMENT),
+    getFileSampleAndName: getFileSampleAndNameDefault,
+  },
   [sampleTech.RHAPSODY]: {
     acceptedFiles: new Set(['expression_data.st', 'expression_data.st.gz']),
     requiredFiles: ['rhapsody'],
diff --git a/src/utils/upload/sampleValidators.js b/src/utils/upload/sampleValidators.js
index e7a28949d3..b679f1a313 100644
--- a/src/utils/upload/sampleValidators.js
+++ b/src/utils/upload/sampleValidators.js
@@ -2,14 +2,15 @@ import { sampleTech } from 'utils/constants';
 
 import validate10x from 'utils/upload/validate10x';
 import validateRhapsody from 'utils/upload/validateRhapsody';
-import validateSeurat from 'utils/upload/validateSeurat';
+import validateObj2s from 'utils/upload/validateObj2s';
 import validateH5 from 'utils/upload/validateH5';
 import validateParse from 'utils/upload/validateParse';
 
 const sampleValidators = {
   [sampleTech['10X']]: validate10x,
   [sampleTech.RHAPSODY]: validateRhapsody,
-  [sampleTech.SEURAT]: validateSeurat,
+  [sampleTech.SEURAT]: validateObj2s,
+  [sampleTech.SINGLE_CELL_EXPERIMENT]: validateObj2s,
   [sampleTech.H5]: validateH5,
   [sampleTech.PARSE]: validateParse,
 };
diff --git a/src/utils/upload/validateObj2s.js b/src/utils/upload/validateObj2s.js
new file mode 100644
index 0000000000..0ca352203a
--- /dev/null
+++ b/src/utils/upload/validateObj2s.js
@@ -0,0 +1,5 @@
+const validateObj2s = async () => {
+  // Currently there is no content checking for obj2s files
+};
+
+export default validateObj2s;
diff --git a/src/utils/upload/validateSeurat.js b/src/utils/upload/validateSeurat.js
deleted file mode 100644
index 2f83d34999..0000000000
--- a/src/utils/upload/validateSeurat.js
+++ /dev/null
@@ -1,5 +0,0 @@
-const validateSeurat = async () => {
-  // Currently there is no content checking for H5 files
-};
-
-export default validateSeurat;

From 56d4761f10d5c10ec1b6eddf0ddd9acf5685509b Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Tue, 17 Sep 2024 13:13:35 -0700
Subject: [PATCH 2/7] fix missed seurat renamings

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 .../components/ContentWrapper.test.jsx        |  2 +-
 .../LaunchAnalysisButton.test.jsx             | 42 ++++++++--------
 .../data-management/ProjectDetails.test.jsx   | 12 ++---
 .../DownloadDataButton.test.jsx.snap          |  2 +-
 .../data/__snapshots__/mockData.test.js.snap  | 48 +++++++++----------
 src/__test__/data/backend_status.json         |  6 +--
 .../switchExperiment.test.js.snap             | 24 +++++-----
 .../mockData/generateMockExperiments.js       |  6 +--
 .../experimentUpdatesHandler.test.js.snap     | 14 +++---
 .../utils/experimentUpdatesHandler.test.js    |  8 ++--
 .../processSampleUpload.obj2s.test.js.snap    | 15 ++++++
 ...t.js => processSampleUpload.obj2s.test.js} |  8 ++--
 src/components/ContentWrapper.jsx             |  8 ++--
 .../data-management/DownloadDataButton.jsx    |  2 +-
 .../data-management/LaunchAnalysisButton.jsx  |  2 +-
 src/redux/actions/pipeline/runObj2s.js        |  2 +-
 src/utils/experimentUpdatesHandler.js         |  4 +-
 .../downloadProcessedMatrix.js                |  3 +-
 18 files changed, 112 insertions(+), 96 deletions(-)
 create mode 100644 src/__test__/utils/upload/__snapshots__/processSampleUpload.obj2s.test.js.snap
 rename src/__test__/utils/upload/{processSampleUpload.seurat.test.js => processSampleUpload.obj2s.test.js} (98%)

diff --git a/src/__test__/components/ContentWrapper.test.jsx b/src/__test__/components/ContentWrapper.test.jsx
index 4d21ab9f95..9ef5d3eaad 100644
--- a/src/__test__/components/ContentWrapper.test.jsx
+++ b/src/__test__/components/ContentWrapper.test.jsx
@@ -220,7 +220,7 @@ describe('ContentWrapper', () => {
           status: 'SUCCEEDED',
           shouldRerun: false,
         },
-        seurat: {
+        obj2s: {
           status: 'NOT_CREATED',
         },
       },
diff --git a/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx b/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
index 2f07e00238..a304cb0084 100644
--- a/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
+++ b/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
@@ -80,7 +80,7 @@ const noDataState = {
           shouldRerun: null,
           status: PipelineStatus.NOT_CREATED,
         },
-        seurat: {
+        obj2s: {
           shouldRerun: null,
           status: PipelineStatus.NOT_CREATED,
         },
@@ -143,7 +143,7 @@ const withDataState = {
           shouldRerun: null,
           status: PipelineStatus.SUCCEEDED,
         },
-        seurat: {
+        obj2s: {
           shouldRerun: null,
           status: PipelineStatus.NOT_CREATED,
         },
@@ -152,7 +152,7 @@ const withDataState = {
   },
 };
 
-const withSeuratDataState = {
+const withObj2sDataState = {
   ...noDataState,
   experiments: {
     ...noDataState.experiments,
@@ -188,7 +188,7 @@ const withSeuratDataState = {
           shouldRerun: null,
           status: PipelineStatus.NOT_CREATED,
         },
-        seurat: {
+        obj2s: {
           shouldRerun: false,
           status: PipelineStatus.SUCCEEDED,
         },
@@ -308,15 +308,15 @@ describe('LaunchAnalysisButton', () => {
     expect(button).toBeDisabled();
   });
 
-  it('Process project button is disabled if not all Seurat data is uploaded', async () => {
-    const notAllSeuratDataUploaded = {
-      ...withSeuratDataState,
+  it('Process project button is disabled if not all Obj2s data is uploaded', async () => {
+    const notAllObj2sDataUploaded = {
+      ...withObj2sDataState,
       samples: {
-        ...withSeuratDataState.samples,
+        ...withObj2sDataState.samples,
         [sample1Uuid]: {
-          ...withSeuratDataState.samples[sample1Uuid],
+          ...withObj2sDataState.samples[sample1Uuid],
           files: {
-            ...withSeuratDataState.samples[sample1Uuid].files,
+            ...withObj2sDataState.samples[sample1Uuid].files,
             'r.rds': { valid: true, upload: { status: UploadStatus.UPLOADING } },
           },
         },
@@ -325,7 +325,7 @@ describe('LaunchAnalysisButton', () => {
 
     await act(async () => {
       render(
-        <Provider store={mockStore(notAllSeuratDataUploaded)}>
+        <Provider store={mockStore(notAllObj2sDataUploaded)}>
           <LaunchAnalysisButton />
         </Provider>,
       );
@@ -353,10 +353,10 @@ describe('LaunchAnalysisButton', () => {
     expect(button).not.toBeDisabled();
   });
 
-  it('Process project button is enabled if all Seurat data is uploaded', async () => {
+  it('Process project button is enabled if all Obj2s data is uploaded', async () => {
     await act(async () => {
       render(
-        <Provider store={mockStore(withSeuratDataState)}>
+        <Provider store={mockStore(withObj2sDataState)}>
           <LaunchAnalysisButton />
         </Provider>,
       );
@@ -384,13 +384,13 @@ describe('LaunchAnalysisButton', () => {
     });
   });
 
-  it('Shows Go to Data Exploration if there are no changes to the Seurat experiment (same hash)', async () => {
+  it('Shows Go to Data Exploration if there are no changes to the Obj2s experiment (same hash)', async () => {
     calculateGem2sRerunStatus.mockReturnValue(notRerunState);
     calculateQCRerunStatus.mockReturnValue(notRerunState);
 
     await act(async () => {
       render(
-        <Provider store={mockStore(withSeuratDataState)}>
+        <Provider store={mockStore(withObj2sDataState)}>
           <LaunchAnalysisButton />
         </Provider>,
       );
@@ -418,13 +418,13 @@ describe('LaunchAnalysisButton', () => {
     });
   });
 
-  it('Shows Process project if there are changes to the Seurat experiment (shouldRerun = true)', async () => {
+  it('Shows Process project if there are changes to the Obj2s experiment (shouldRerun = true)', async () => {
     calculateGem2sRerunStatus.mockReturnValue(rerunState);
     calculateQCRerunStatus.mockReturnValue(notRerunState);
 
     await act(async () => {
       render(
-        <Provider store={mockStore(withSeuratDataState)}>
+        <Provider store={mockStore(withObj2sDataState)}>
           <LaunchAnalysisButton />
         </Provider>,
       );
@@ -499,11 +499,11 @@ describe('LaunchAnalysisButton', () => {
     calculateGem2sRerunStatus.mockReturnValue(rerunState);
     calculateQCRerunStatus.mockReturnValue(notRerunState);
 
-    const notProcessedSeuratDataState = {
-      ...withSeuratDataState,
+    const notProcessedObj2sDataState = {
+      ...withObj2sDataState,
       backendStatus: {
         ...noDataState.backendStatus,
-        seurat: {
+        obj2s: {
           status: PipelineStatus.NOT_CREATED,
           shouldRerun: true,
         },
@@ -512,7 +512,7 @@ describe('LaunchAnalysisButton', () => {
 
     await act(async () => {
       render(
-        <Provider store={mockStore(notProcessedSeuratDataState)}>
+        <Provider store={mockStore(notProcessedObj2sDataState)}>
           <LaunchAnalysisButton />
         </Provider>,
       );
diff --git a/src/__test__/components/data-management/ProjectDetails.test.jsx b/src/__test__/components/data-management/ProjectDetails.test.jsx
index 6855d58f9c..814b111b72 100644
--- a/src/__test__/components/data-management/ProjectDetails.test.jsx
+++ b/src/__test__/components/data-management/ProjectDetails.test.jsx
@@ -93,7 +93,7 @@ const noDataState = {
         pipeline: {
           status: PipelineStatus.NOT_CREATED,
         },
-        seurat: {
+        obj2s: {
           status: PipelineStatus.NOT_CREATED,
         },
       },
@@ -154,7 +154,7 @@ const withDataState = {
         pipeline: {
           status: PipelineStatus.SUCCEEDED,
         },
-        seurat: {
+        obj2s: {
           status: PipelineStatus.NOT_CREATED,
         },
       },
@@ -162,7 +162,7 @@ const withDataState = {
   },
 };
 
-const withSeuratDataState = {
+const withObj2sDataState = {
   ...noDataState,
   experiments: {
     ...noDataState.experiments,
@@ -195,7 +195,7 @@ const withSeuratDataState = {
         pipeline: {
           status: PipelineStatus.NOT_CREATED,
         },
-        seurat: {
+        obj2s: {
           paramsHash: 'old-params-hash',
           status: PipelineStatus.SUCCEEDED,
         },
@@ -288,9 +288,9 @@ describe('ProjectDetails', () => {
     expect(metadataButton).not.toBeDisabled();
   });
 
-  it('metadata button is disabled if it is Seurat', () => {
+  it('metadata button is disabled if it is Obj2s', () => {
     render(
-      <Provider store={mockStore(withSeuratDataState)}>
+      <Provider store={mockStore(withObj2sDataState)}>
         {projectDetailsFactory()}
       </Provider>,
     );
diff --git a/src/__test__/components/data-management/__snapshots__/DownloadDataButton.test.jsx.snap b/src/__test__/components/data-management/__snapshots__/DownloadDataButton.test.jsx.snap
index a0fa4b07ed..68f7f5b202 100644
--- a/src/__test__/components/data-management/__snapshots__/DownloadDataButton.test.jsx.snap
+++ b/src/__test__/components/data-management/__snapshots__/DownloadDataButton.test.jsx.snap
@@ -23,7 +23,7 @@ exports[`DownloadDataButton Downloads processed matrix properly 1`] = `
     "testae48e318dab9a1bd0bexperiment-0",
     {
       "embeddingMethod": "umap",
-      "isSeurat": false,
+      "isObj2s": false,
       "name": "DownloadAnnotSeuratObject",
     },
     [Function],
diff --git a/src/__test__/data/__snapshots__/mockData.test.js.snap b/src/__test__/data/__snapshots__/mockData.test.js.snap
index d15f4ced79..45b692e727 100644
--- a/src/__test__/data/__snapshots__/mockData.test.js.snap
+++ b/src/__test__/data/__snapshots__/mockData.test.js.snap
@@ -23,10 +23,10 @@ exports[`Mock data Describes samples 1`] = `
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "samplesOrder": [
@@ -87,10 +87,10 @@ exports[`Mock data Describes samples 1`] = `
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "samplesOrder": [
@@ -151,10 +151,10 @@ exports[`Mock data Describes samples 1`] = `
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "samplesOrder": [
@@ -218,10 +218,10 @@ exports[`Mock response data Describes experiment response 1`] = `
         "shouldRerun": null,
         "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
-      "seurat": {
-        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+      "obj2s": {
+        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
         "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
     },
     "samplesOrder": [
@@ -250,10 +250,10 @@ exports[`Mock response data Describes experiment response 1`] = `
         "shouldRerun": null,
         "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
-      "seurat": {
-        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+      "obj2s": {
+        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
         "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
     },
     "samplesOrder": [],
@@ -286,10 +286,10 @@ exports[`Mock response data Describes samples response 1`] = `
             "shouldRerun": null,
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
-          "seurat": {
-            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+          "obj2s": {
+            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
             "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
         },
         "samplesOrder": [
@@ -350,10 +350,10 @@ exports[`Mock response data Describes samples response 1`] = `
             "shouldRerun": null,
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
-          "seurat": {
-            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+          "obj2s": {
+            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
             "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
         },
         "samplesOrder": [
@@ -414,10 +414,10 @@ exports[`Mock response data Describes samples response 1`] = `
             "shouldRerun": null,
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
-          "seurat": {
-            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+          "obj2s": {
+            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
             "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
         },
         "samplesOrder": [
diff --git a/src/__test__/data/backend_status.json b/src/__test__/data/backend_status.json
index 4656dae4ab..7fae40386d 100644
--- a/src/__test__/data/backend_status.json
+++ b/src/__test__/data/backend_status.json
@@ -35,15 +35,15 @@
     "executionArn": "arn:aws:states:eu-east-1:000000000000:execution:biomage-gem2s-test-test9cd23b9138d3d5b6141835c85101495a92cd:fb047b29-a9fb-4e36-a0fc-b792e243test",
     "stateMachineArn": "arn:aws:states:eu-east-1:000000000000:stateMachine:biomage-gem2s-test-test9cd23b9138d3d5b6141835c85101495atest"
   },
-  "seurat": {
+  "obj2s": {
     "startDate": "2021-10-20T12:49:06.414Z",
     "stopDate": "2021-10-20T12:51:44.081Z",
     "status": "NOT_CREATED",
     "error": false,
     "completedSteps": [],
     "paramsHash": "2a0a9cdca259ce91207cbe62574ba6f4851cfake", 
-    "executionArn": "arn:aws:states:eu-east-1:000000000000:execution:biomage-seurat-test-test9cd23b9138d3d5b6141835c85101495a92cd:fb047b29-a9fb-4e36-a0fc-b792e243test",
-    "stateMachineArn": "arn:aws:states:eu-east-1:000000000000:stateMachine:biomage-seurat-test-test9cd23b9138d3d5b6141835c85101495atest"
+    "executionArn": "arn:aws:states:eu-east-1:000000000000:execution:biomage-obj2s-test-test9cd23b9138d3d5b6141835c85101495a92cd:fb047b29-a9fb-4e36-a0fc-b792e243test",
+    "stateMachineArn": "arn:aws:states:eu-east-1:000000000000:stateMachine:biomage-obj2s-test-test9cd23b9138d3d5b6141835c85101495atest"
   },
   "worker": {
     "status": "Running",
diff --git a/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap b/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap
index cb702417eb..5d4c8022f4 100644
--- a/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap
+++ b/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap
@@ -128,10 +128,10 @@ exports[`switch experiment  Then updates the experiment info 1`] = `
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "sampleIds": [
@@ -160,10 +160,10 @@ exports[`switch experiment  Then updates the experiment info 1`] = `
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "sampleIds": [],
@@ -559,10 +559,10 @@ exports[`switch experiment  switches the experiment to its initial values 1`] =
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "sampleIds": [
@@ -591,10 +591,10 @@ exports[`switch experiment  switches the experiment to its initial values 1`] =
           "shouldRerun": null,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "seurat": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
+        "obj2s": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
       },
       "sampleIds": [],
diff --git a/src/__test__/test-utils/mockData/generateMockExperiments.js b/src/__test__/test-utils/mockData/generateMockExperiments.js
index a0712df609..66beadbfc3 100644
--- a/src/__test__/test-utils/mockData/generateMockExperiments.js
+++ b/src/__test__/test-utils/mockData/generateMockExperiments.js
@@ -19,10 +19,10 @@ const experimentFromTemplate = (idx) => (
         stateMachineArn: 'arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test',
         executionArn: 'arn:aws:states:eu-west-1:000000000000:execution:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test',
       },
-      seurat: {
+      obj2s: {
         paramsHash: 'mock57f90e94eeaa82ee6fb7627110828f2etest',
-        stateMachineArn: 'arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec151test',
-        executionArn: 'arn:aws:states:eu-west-1:000000000000:execution:biomage-seurat-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test',
+        stateMachineArn: 'arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test',
+        executionArn: 'arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test',
       },
     },
     notifyByEmail: true,
diff --git a/src/__test__/utils/__snapshots__/experimentUpdatesHandler.test.js.snap b/src/__test__/utils/__snapshots__/experimentUpdatesHandler.test.js.snap
index 628d8050b1..48276142fc 100644
--- a/src/__test__/utils/__snapshots__/experimentUpdatesHandler.test.js.snap
+++ b/src/__test__/utils/__snapshots__/experimentUpdatesHandler.test.js.snap
@@ -111,18 +111,18 @@ exports[`ExperimentUpdatesHandler Loads cell sets if QC pipeline completes  4`]
 ]
 `;
 
-exports[`ExperimentUpdatesHandler Loads cell sets if Seurat pipeline completes  1`] = `
+exports[`ExperimentUpdatesHandler Loads cell sets if Obj2s pipeline completes  1`] = `
 [
   "testae48e318dab9a1bd0bexperiment",
   {
-    "seurat": {
+    "obj2s": {
       "status": "SUCCEEDED",
     },
   },
 ]
 `;
 
-exports[`ExperimentUpdatesHandler Loads cell sets if Seurat pipeline completes  2`] = `
+exports[`ExperimentUpdatesHandler Loads cell sets if Obj2s pipeline completes  2`] = `
 [
   "testae48e318dab9a1bd0bexperiment",
   true,
@@ -182,22 +182,22 @@ exports[`ExperimentUpdatesHandler Triggers properly for QC updates  4`] = `
 ]
 `;
 
-exports[`ExperimentUpdatesHandler Triggers properly for SEURAT updates  1`] = `
+exports[`ExperimentUpdatesHandler Triggers properly for OBJ2S updates  1`] = `
 [
   "testae48e318dab9a1bd0bexperiment",
   {
-    "seurat": {
+    "obj2s": {
       "status": "RUNNING",
     },
   },
 ]
 `;
 
-exports[`ExperimentUpdatesHandler Triggers properly for SEURAT updates  2`] = `
+exports[`ExperimentUpdatesHandler Triggers properly for OBJ2S updates  2`] = `
 [
   "testae48e318dab9a1bd0bexperiment",
   {
-    "seurat": {
+    "obj2s": {
       "status": "RUNNING",
     },
   },
diff --git a/src/__test__/utils/experimentUpdatesHandler.test.js b/src/__test__/utils/experimentUpdatesHandler.test.js
index 698cd1f317..49ae4f4308 100644
--- a/src/__test__/utils/experimentUpdatesHandler.test.js
+++ b/src/__test__/utils/experimentUpdatesHandler.test.js
@@ -102,7 +102,7 @@ const mockObj2sUpdate = {
     },
   },
   status: {
-    seurat: {
+    obj2s: {
       status: 'RUNNING',
     },
   },
@@ -158,11 +158,11 @@ describe('ExperimentUpdatesHandler', () => {
     expect(mockDispatch).toHaveBeenCalledTimes(1);
   });
 
-  it('Loads cell sets if Seurat pipeline completes ', () => {
+  it('Loads cell sets if Obj2s pipeline completes ', () => {
     const mockUpdate = {
       ...mockObj2sUpdate,
       status: {
-        seurat: {
+        obj2s: {
           status: 'SUCCEEDED',
         },
       },
@@ -175,7 +175,7 @@ describe('ExperimentUpdatesHandler', () => {
     const backendStatus = updateBackendStatus.mock.calls[0];
     expect(backendStatus).toMatchSnapshot();
 
-    // Dispatch 2 - load cellsets on seurat finish
+    // Dispatch 2 - load cellsets on obj2s finish
     expect(loadCellSets).toHaveBeenCalledTimes(1);
     const loadCellSetsParams = loadCellSets.mock.calls[0];
     expect(loadCellSetsParams).toMatchSnapshot();
diff --git a/src/__test__/utils/upload/__snapshots__/processSampleUpload.obj2s.test.js.snap b/src/__test__/utils/upload/__snapshots__/processSampleUpload.obj2s.test.js.snap
new file mode 100644
index 0000000000..de03ec4935
--- /dev/null
+++ b/src/__test__/utils/upload/__snapshots__/processSampleUpload.obj2s.test.js.snap
@@ -0,0 +1,15 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`processUpload Uploads and updates redux correctly when there are no errors 1`] = `
+[
+  {
+    "headers": {
+      "Content-Type": "application/octet-stream",
+    },
+    "method": "put",
+    "onUploadProgress": [Function],
+    "signal": AbortSignal {},
+    "url": "theSignedUrl",
+  },
+]
+`;
diff --git a/src/__test__/utils/upload/processSampleUpload.seurat.test.js b/src/__test__/utils/upload/processSampleUpload.obj2s.test.js
similarity index 98%
rename from src/__test__/utils/upload/processSampleUpload.seurat.test.js
rename to src/__test__/utils/upload/processSampleUpload.obj2s.test.js
index fbab3f0557..f43b10bc98 100644
--- a/src/__test__/utils/upload/processSampleUpload.seurat.test.js
+++ b/src/__test__/utils/upload/processSampleUpload.obj2s.test.js
@@ -16,7 +16,7 @@ import UploadStatus from 'utils/upload/UploadStatus';
 
 import processSampleUpload from 'utils/upload/processSampleUpload';
 
-import validate from 'utils/upload/validateSeurat';
+import validate from 'utils/upload/validateObj2s';
 import pushNotificationMessage from 'utils/pushNotificationMessage';
 import mockFile from '__test__/test-utils/mockFile';
 
@@ -28,7 +28,7 @@ jest.mock('../../../utils/upload/fileUploadConfig', () => ({
 enableFetchMocks();
 
 const getValidFiles = (fileSize = 1 * MB) => {
-  const seuratFiles = [{
+  const obj2sFiles = [{
     name: 'r.rds',
     fileObject: mockFile('r.rds', '', fileSize),
     size: fileSize,
@@ -38,7 +38,7 @@ const getValidFiles = (fileSize = 1 * MB) => {
     valid: true,
   }];
 
-  return seuratFiles;
+  return obj2sFiles;
 };
 
 const sampleType = sampleTech.SEURAT;
@@ -81,7 +81,7 @@ jest.mock('axios', () => ({
 }));
 
 jest.mock('utils/pushNotificationMessage');
-jest.mock('utils/upload/validateSeurat');
+jest.mock('utils/upload/validateObj2s');
 
 let store = null;
 
diff --git a/src/components/ContentWrapper.jsx b/src/components/ContentWrapper.jsx
index de4bd62f5c..ecf579493f 100644
--- a/src/components/ContentWrapper.jsx
+++ b/src/components/ContentWrapper.jsx
@@ -105,14 +105,14 @@ const ContentWrapper = (props) => {
   const gem2sRunning = gem2sStatusKey === 'RUNNING';
   const gem2sRunningError = backendErrors.includes(gem2sStatusKey);
   const completedGem2sSteps = backendStatus?.gem2s?.completedSteps;
-  const obj2sStatusKey = backendStatus?.seurat?.status;
+  const obj2sStatusKey = backendStatus?.obj2s?.status;
 
   const isObj2s = obj2sStatusKey && obj2sTechs.includes(selectedTechnology);
 
   const [pipelinesRerunStatus, setPipelinesRerunStatus] = useState(null);
   const obj2sRunning = obj2sStatusKey === 'RUNNING' && isObj2s;
   const obj2sRunningError = backendErrors.includes(obj2sStatusKey) && isObj2s;
-  const completedObj2sSteps = backendStatus?.seurat?.completedSteps;
+  const completedObj2sSteps = backendStatus?.obj2s?.completedSteps;
   const obj2sComplete = (obj2sStatusKey === pipelineStatusValues.SUCCEEDED) && isObj2s;
   const waitingForQcToLaunch = gem2sStatusKey === pipelineStatusValues.SUCCEEDED
     && qcStatusKey === pipelineStatusValues.NOT_CREATED;
@@ -154,7 +154,7 @@ const ContentWrapper = (props) => {
     if (!experiment || !backendStatus) return;
 
     // The value of backend status is null for new experiments that have never run
-    const setupPipeline = isObj2s ? 'seurat' : 'gem2s';
+    const setupPipeline = isObj2s ? 'obj2s' : 'gem2s';
     const {
       pipeline: qcBackendStatus, [setupPipeline]: setupBackendStatus,
     } = backendStatus ?? {};
@@ -192,7 +192,7 @@ const ContentWrapper = (props) => {
 
   const getObj2sStatus = () => {
     if (obj2sRunningError) {
-      const errorMessage = pipelineErrorUserMessages[backendStatus?.seurat?.error?.error];
+      const errorMessage = pipelineErrorUserMessages[backendStatus?.obj2s?.error?.error];
       return getStatusObject('obj2s', 'error', errorMessage);
     }
     if (obj2sRunning) {
diff --git a/src/components/data-management/DownloadDataButton.jsx b/src/components/data-management/DownloadDataButton.jsx
index d8ab5c4c93..7a83f0176f 100644
--- a/src/components/data-management/DownloadDataButton.jsx
+++ b/src/components/data-management/DownloadDataButton.jsx
@@ -45,7 +45,7 @@ const DownloadDataButton = () => {
   useEffect(() => {
     setPipelineHasRun(
       activeExperimentId && (backendStatuses?.pipeline?.status === pipelineStatus.SUCCEEDED
-        || backendStatuses?.seurat?.status === pipelineStatus.SUCCEEDED),
+        || backendStatuses?.obj2s?.status === pipelineStatus.SUCCEEDED),
     );
   }, [backendStatuses]);
 
diff --git a/src/components/data-management/LaunchAnalysisButton.jsx b/src/components/data-management/LaunchAnalysisButton.jsx
index b4dbe69900..bc9383e765 100644
--- a/src/components/data-management/LaunchAnalysisButton.jsx
+++ b/src/components/data-management/LaunchAnalysisButton.jsx
@@ -48,7 +48,7 @@ const LaunchAnalysisButton = () => {
 
   useEffect(() => {
     // The value of backend status is null for new experiments that have never run
-    const setupPipeline = isObj2s ? 'seurat' : 'gem2s';
+    const setupPipeline = isObj2s ? 'obj2s' : 'gem2s';
     const {
       pipeline: qcBackendStatus, [setupPipeline]: setupBackendStatus,
     } = backendStatus[activeExperimentId]?.status ?? {};
diff --git a/src/redux/actions/pipeline/runObj2s.js b/src/redux/actions/pipeline/runObj2s.js
index 3ad03f4a7b..8fb21fa20e 100644
--- a/src/redux/actions/pipeline/runObj2s.js
+++ b/src/redux/actions/pipeline/runObj2s.js
@@ -6,7 +6,7 @@ import loadBackendStatus from 'redux/actions/backendStatus/loadBackendStatus';
 const runObj2s = (experimentId) => async (dispatch) => {
   try {
     await fetchAPI(
-      `/v2/experiments/${experimentId}/seurat`,
+      `/v2/experiments/${experimentId}/obj2s`,
       {
         method: 'POST',
         headers: {
diff --git a/src/utils/experimentUpdatesHandler.js b/src/utils/experimentUpdatesHandler.js
index 492dbd6153..af272f663c 100644
--- a/src/utils/experimentUpdatesHandler.js
+++ b/src/utils/experimentUpdatesHandler.js
@@ -12,7 +12,7 @@ import endUserMessages from 'utils/endUserMessages';
 const updateTypes = {
   QC: 'qc',
   GEM2S: 'gem2s',
-  OBJ2S: 'seurat',
+  OBJ2S: 'obj2s',
   WORK_RESPONSE: 'WorkResponse',
   PLOT_CONFIG_REFRESH: 'PlotConfigRefresh',
 };
@@ -118,7 +118,7 @@ const onPlotConfigRefresh = (update, dispatch) => {
 
 const onObj2sUpdate = (update, dispatch, experimentId) => {
   // If the pipeline finished we have a new clustering, so fetch it
-  if (update.status.seurat.status === 'SUCCEEDED') {
+  if (update.status.obj2s.status === 'SUCCEEDED') {
     dispatch(loadCellSets(experimentId, true));
   }
 };
diff --git a/src/utils/extraActionCreators/downloadProcessedMatrix.js b/src/utils/extraActionCreators/downloadProcessedMatrix.js
index 2460707227..fa459e5e7e 100644
--- a/src/utils/extraActionCreators/downloadProcessedMatrix.js
+++ b/src/utils/extraActionCreators/downloadProcessedMatrix.js
@@ -14,7 +14,8 @@ const downloadProcessedMatrix = (experimentId) => async (dispatch, getState) =>
 
     const {
       method: embeddingMethod,
-      // embedding is saved in R object if downloading from project created by Seurat/SingleCellExperiment object upload
+      // embedding is saved in R object if downloading from project created by
+      // Seurat/SingleCellExperiment object upload
       useSaved,
     } = getState().experimentSettings.processing.configureEmbedding.embeddingSettings;
 

From e4b49dbec68136516e78b50e94d9a78a22d089b9 Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Tue, 17 Sep 2024 13:22:05 -0700
Subject: [PATCH 3/7] update snaps

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 .../data-management/FileUploadModal.test.jsx  |  2 +-
 .../data/__snapshots__/mockData.test.js.snap  | 80 +++++++++----------
 .../switchExperiment.test.js.snap             | 40 +++++-----
 .../processSampleUpload.seurat.test.js.snap   | 15 ----
 4 files changed, 61 insertions(+), 76 deletions(-)
 delete mode 100644 src/__test__/utils/upload/__snapshots__/processSampleUpload.seurat.test.js.snap

diff --git a/src/__test__/components/data-management/FileUploadModal.test.jsx b/src/__test__/components/data-management/FileUploadModal.test.jsx
index e28ab8aeb3..daa246f6cc 100644
--- a/src/__test__/components/data-management/FileUploadModal.test.jsx
+++ b/src/__test__/components/data-management/FileUploadModal.test.jsx
@@ -360,7 +360,7 @@ describe('FileUploadModal', () => {
     expect(uploadButton).toBeDisabled();
 
     // error message was displayed to user
-    expect(handleError).toHaveBeenCalledWith('error', endUserMessages.ERROR_SEURAT_EXISTING_FILE);
+    expect(handleError).toHaveBeenCalledWith('error', endUserMessages.ERROR_OBJ2S_EXISTING_FILE);
   });
 
   it('Shows what files can be uploaded for Rhapsody samples', async () => {
diff --git a/src/__test__/data/__snapshots__/mockData.test.js.snap b/src/__test__/data/__snapshots__/mockData.test.js.snap
index 45b692e727..5208ae18b6 100644
--- a/src/__test__/data/__snapshots__/mockData.test.js.snap
+++ b/src/__test__/data/__snapshots__/mockData.test.js.snap
@@ -18,16 +18,16 @@ exports[`Mock data Describes samples 1`] = `
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "samplesOrder": [
         "test9188-d682-test-mock-cb6d644cmock-0",
@@ -82,16 +82,16 @@ exports[`Mock data Describes samples 1`] = `
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "samplesOrder": [
         "test9188-d682-test-mock-cb6d644cmock-0",
@@ -146,16 +146,16 @@ exports[`Mock data Describes samples 1`] = `
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "samplesOrder": [
         "test9188-d682-test-mock-cb6d644cmock-0",
@@ -213,16 +213,16 @@ exports[`Mock response data Describes experiment response 1`] = `
         "shouldRerun": true,
         "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
-      "qc": {
-        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-        "shouldRerun": null,
-        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-      },
       "obj2s": {
         "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
         "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
         "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
+      "qc": {
+        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+        "shouldRerun": null,
+        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+      },
     },
     "samplesOrder": [
       "test9188-d682-test-mock-cb6d644cmock-0",
@@ -245,16 +245,16 @@ exports[`Mock response data Describes experiment response 1`] = `
         "shouldRerun": true,
         "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
-      "qc": {
-        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-        "shouldRerun": null,
-        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-      },
       "obj2s": {
         "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
         "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
         "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
       },
+      "qc": {
+        "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+        "shouldRerun": null,
+        "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+      },
     },
     "samplesOrder": [],
     "updatedAt": "0000-00-00T00:00:00.000Z",
@@ -281,16 +281,16 @@ exports[`Mock response data Describes samples response 1`] = `
             "shouldRerun": true,
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
-          "qc": {
-            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-            "shouldRerun": null,
-            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-          },
           "obj2s": {
             "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
             "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
+          "qc": {
+            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+            "shouldRerun": null,
+            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          },
         },
         "samplesOrder": [
           "test9188-d682-test-mock-cb6d644cmock-0",
@@ -345,16 +345,16 @@ exports[`Mock response data Describes samples response 1`] = `
             "shouldRerun": true,
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
-          "qc": {
-            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-            "shouldRerun": null,
-            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-          },
           "obj2s": {
             "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
             "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
+          "qc": {
+            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+            "shouldRerun": null,
+            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          },
         },
         "samplesOrder": [
           "test9188-d682-test-mock-cb6d644cmock-0",
@@ -409,16 +409,16 @@ exports[`Mock response data Describes samples response 1`] = `
             "shouldRerun": true,
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
-          "qc": {
-            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-            "shouldRerun": null,
-            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-          },
           "obj2s": {
             "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
             "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
             "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
           },
+          "qc": {
+            "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+            "shouldRerun": null,
+            "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+          },
         },
         "samplesOrder": [
           "test9188-d682-test-mock-cb6d644cmock-0",
diff --git a/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap b/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap
index 5d4c8022f4..01c35a1c25 100644
--- a/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap
+++ b/src/__test__/redux/actions/experiments/__snapshots__/switchExperiment.test.js.snap
@@ -123,16 +123,16 @@ exports[`switch experiment  Then updates the experiment info 1`] = `
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "sampleIds": [
         "test9188-d682-test-mock-cb6d644cmock-0",
@@ -155,16 +155,16 @@ exports[`switch experiment  Then updates the experiment info 1`] = `
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "sampleIds": [],
       "updatedAt": "0000-00-00T00:00:00.000Z",
@@ -554,16 +554,16 @@ exports[`switch experiment  switches the experiment to its initial values 1`] =
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "sampleIds": [
         "test9188-d682-test-mock-cb6d644cmock-0",
@@ -586,16 +586,16 @@ exports[`switch experiment  switches the experiment to its initial values 1`] =
           "shouldRerun": true,
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-gem2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
-        "qc": {
-          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
-          "shouldRerun": null,
-          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
-        },
         "obj2s": {
           "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec1519de4:5f273383-f093-4112-95b0-d76db896test",
           "paramsHash": "mock57f90e94eeaa82ee6fb7627110828f2etest",
           "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-obj2s-development-mock997586f1bae0a6d5c5beed65663ec151test",
         },
+        "qc": {
+          "executionArn": "arn:aws:states:eu-west-1:000000000000:execution:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec1519de4:422493f3-68a0-4ecb-8b17-0e8cd7a3test",
+          "shouldRerun": null,
+          "stateMachineArn": "arn:aws:states:eu-west-1:000000000000:stateMachine:biomage-qc-development-mock997586f1bae0a6d5c5beed65663ec151test",
+        },
       },
       "sampleIds": [],
       "updatedAt": "0000-00-00T00:00:00.000Z",
diff --git a/src/__test__/utils/upload/__snapshots__/processSampleUpload.seurat.test.js.snap b/src/__test__/utils/upload/__snapshots__/processSampleUpload.seurat.test.js.snap
deleted file mode 100644
index de03ec4935..0000000000
--- a/src/__test__/utils/upload/__snapshots__/processSampleUpload.seurat.test.js.snap
+++ /dev/null
@@ -1,15 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`processUpload Uploads and updates redux correctly when there are no errors 1`] = `
-[
-  {
-    "headers": {
-      "Content-Type": "application/octet-stream",
-    },
-    "method": "put",
-    "onUploadProgress": [Function],
-    "signal": AbortSignal {},
-    "url": "theSignedUrl",
-  },
-]
-`;

From c6f0dceac5b7a77848c6f91f7062ba4b98bd1eac Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Tue, 17 Sep 2024 15:10:13 -0700
Subject: [PATCH 4/7] renaming things

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 .../data-management/FileUploadModal.test.jsx  | 12 +++++------
 .../LaunchAnalysisButton.test.jsx             |  2 +-
 .../data-management/ProjectDetails.test.jsx   |  2 +-
 .../utils/upload/fileInspector.test.js        |  4 ++--
 .../upload/processSampleUpload.obj2s.test.js  |  2 +-
 .../data-management/FileUploadModal.jsx       |  4 ++--
 src/utils/constants.js                        |  6 +++---
 src/utils/sampleFileType.js                   |  8 ++++----
 src/utils/upload/fileUploadUtils.js           | 20 +++++++++----------
 src/utils/upload/sampleValidators.js          |  4 ++--
 10 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/src/__test__/components/data-management/FileUploadModal.test.jsx b/src/__test__/components/data-management/FileUploadModal.test.jsx
index daa246f6cc..62e223be85 100644
--- a/src/__test__/components/data-management/FileUploadModal.test.jsx
+++ b/src/__test__/components/data-management/FileUploadModal.test.jsx
@@ -64,7 +64,7 @@ const renderFileUploadModal = async (store, currentSelectedTech = null) => {
   )));
 };
 
-const seuratTech = techNamesToDisplay[sampleTech.SEURAT];
+const seuratTech = techNamesToDisplay[sampleTech.SEURAT_OBJECT];
 
 const selectTech = (selectedTech) => {
   const displayedName = techNamesToDisplay[selectedTech];
@@ -126,7 +126,7 @@ describe('FileUploadModal', () => {
     expect(screen.queryAllByText(techNamesToDisplay[sampleTech['10X']]).length).toBe(1);
     expect(screen.queryAllByText(seuratTech).length).toBe(0);
 
-    selectTech(sampleTech.SEURAT);
+    selectTech(sampleTech.SEURAT_OBJECT);
 
     // Lists the requirements of the Seurat object
     expect(screen.getByText(/The Seurat object must contain the following slots and metadata:/i)).toBeInTheDocument();
@@ -203,7 +203,7 @@ describe('FileUploadModal', () => {
   it('drag and drop works with valid Seurat file', async () => {
     await renderFileUploadModal(initialStore);
 
-    selectTech(sampleTech.SEURAT);
+    selectTech(sampleTech.SEURAT_OBJECT);
 
     expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
 
@@ -240,7 +240,7 @@ describe('FileUploadModal', () => {
   it('drag and drop works with valid Seurat file when different experiment has valid uploaded Seurat object', async () => {
     await renderFileUploadModal(prevUpDiffExpStore);
 
-    selectTech(sampleTech.SEURAT);
+    selectTech(sampleTech.SEURAT_OBJECT);
 
     expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
 
@@ -284,7 +284,7 @@ describe('FileUploadModal', () => {
 
     expect(techInput).toBeEnabled();
 
-    selectTech(sampleTech.SEURAT);
+    selectTech(sampleTech.SEURAT_OBJECT);
 
     expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
 
@@ -317,7 +317,7 @@ describe('FileUploadModal', () => {
   });
 
   it('drag and drop fails with valid Seurat file when pre-existing Seurat file exists for experiment', async () => {
-    await renderFileUploadModal(prevUpStore, sampleTech.SEURAT);
+    await renderFileUploadModal(prevUpStore, sampleTech.SEURAT_OBJECT);
 
     // Seurat info should show up as their is previous Seurat data uploaded
     await waitFor(() => expect(
diff --git a/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx b/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
index a304cb0084..1072fab6a9 100644
--- a/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
+++ b/src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
@@ -169,7 +169,7 @@ const withObj2sDataState = {
       name: sample1Name,
       experimentId: experiment1id,
       uuid: sample1Uuid,
-      type: sampleTech.SEURAT,
+      type: sampleTech.SEURAT_OBJECT,
       fileNames: ['r.rds'],
       files: {
         'r.rds': { valid: true, upload: { status: UploadStatus.UPLOADED } },
diff --git a/src/__test__/components/data-management/ProjectDetails.test.jsx b/src/__test__/components/data-management/ProjectDetails.test.jsx
index 814b111b72..0a4c45d331 100644
--- a/src/__test__/components/data-management/ProjectDetails.test.jsx
+++ b/src/__test__/components/data-management/ProjectDetails.test.jsx
@@ -178,7 +178,7 @@ const withObj2sDataState = {
       name: sample1Name,
       experimentId: experiment1id,
       uuid: sample1Uuid,
-      type: sampleTech.SEURAT,
+      type: sampleTech.SEURAT_OBJECT,
       fileNames: ['r.rds'],
       files: {
         'r.rds': { valid: true, upload: { status: UploadStatus.UPLOADED } },
diff --git a/src/__test__/utils/upload/fileInspector.test.js b/src/__test__/utils/upload/fileInspector.test.js
index 58f6b1d50f..783f70316e 100644
--- a/src/__test__/utils/upload/fileInspector.test.js
+++ b/src/__test__/utils/upload/fileInspector.test.js
@@ -185,7 +185,7 @@ describe('fileInspector', () => {
       name: 'scdata.rds',
     };
 
-    expect(await inspectFile(file, sampleTech.SEURAT))
+    expect(await inspectFile(file, sampleTech.SEURAT_OBJECT))
       .toEqual(Verdict.VALID_ZIPPED);
   });
 
@@ -194,7 +194,7 @@ describe('fileInspector', () => {
       name: 'blah.txt',
     };
 
-    expect(await inspectFile(file, sampleTech.SEURAT))
+    expect(await inspectFile(file, sampleTech.SEURAT_OBJECT))
       .toEqual(Verdict.INVALID_NAME);
   });
 });
diff --git a/src/__test__/utils/upload/processSampleUpload.obj2s.test.js b/src/__test__/utils/upload/processSampleUpload.obj2s.test.js
index f43b10bc98..16514a1af8 100644
--- a/src/__test__/utils/upload/processSampleUpload.obj2s.test.js
+++ b/src/__test__/utils/upload/processSampleUpload.obj2s.test.js
@@ -41,7 +41,7 @@ const getValidFiles = (fileSize = 1 * MB) => {
   return obj2sFiles;
 };
 
-const sampleType = sampleTech.SEURAT;
+const sampleType = sampleTech.SEURAT_OBJECT;
 const mockSampleUuid = 'sample-uuid';
 const mockExperimentId = 'project-uuid';
 const sampleName = 'mockSampleName';
diff --git a/src/components/data-management/FileUploadModal.jsx b/src/components/data-management/FileUploadModal.jsx
index 00cc415e24..b9126191ed 100644
--- a/src/components/data-management/FileUploadModal.jsx
+++ b/src/components/data-management/FileUploadModal.jsx
@@ -40,8 +40,8 @@ const OBJ2S_MAX_FILE_SIZE = 15 * 1024 * 1024 * 1024;
 
 const extraHelpText = {
   [sampleTech['10X']]: () => <></>,
-  [sampleTech.SEURAT]: () => <></>,
-  [sampleTech.SINGLE_CELL_EXPERIMENT]: () => <></>,
+  [sampleTech.SEURAT_OBJECT]: () => <></>,
+  [sampleTech.SCE_OBJECT]: () => <></>,
   [sampleTech.H5]: () => <></>,
   [sampleTech.RHAPSODY]: () => (
     <Paragraph>
diff --git a/src/utils/constants.js b/src/utils/constants.js
index 2a3aa84bf6..a8cd5a44e3 100644
--- a/src/utils/constants.js
+++ b/src/utils/constants.js
@@ -18,13 +18,13 @@ const modules = {
 const sampleTech = {
   '10X': '10x',
   RHAPSODY: 'rhapsody',
-  SEURAT: 'seurat',
-  SINGLE_CELL_EXPERIMENT: 'single_cell_experiment',
+  SEURAT_OBJECT: 'seurat_object',
+  SCE_OBJECT: 'sce_object',
   H5: '10x_h5',
   PARSE: 'parse',
 };
 
-const obj2sTechs = [sampleTech.SEURAT, sampleTech.SINGLE_CELL_EXPERIMENT];
+const obj2sTechs = [sampleTech.SEURAT_OBJECT, sampleTech.SCE_OBJECT];
 
 const plotTypes = {
   CONTINUOUS_EMBEDDING: 'embeddingContinuous',
diff --git a/src/utils/sampleFileType.js b/src/utils/sampleFileType.js
index 0ed92340bd..ffcc1242b0 100644
--- a/src/utils/sampleFileType.js
+++ b/src/utils/sampleFileType.js
@@ -3,8 +3,8 @@ const sampleFileType = {
   FEATURES_10_X: 'features10x',
   MATRIX_10_X: 'matrix10x',
   H5_10_X: '10x_h5',
-  SEURAT: 'seurat',
-  SINGLE_CELL_EXPERIMENT: 'single_cell_experiment',
+  SEURAT_OBJECT: 'seurat_object',
+  SCE_OBJECT: 'sce_object',
   RHAPSODY: 'rhapsody',
   FEATURES_PARSE: 'featuresParse',
   BARCODES_PARSE: 'barcodesParse',
@@ -16,8 +16,8 @@ const fileTypeToDisplay = {
   [sampleFileType.FEATURES_10_X]: 'genes.tsv',
   [sampleFileType.MATRIX_10_X]: 'matrix.mtx',
   [sampleFileType.H5_10_X]: 'matrix.h5',
-  [sampleFileType.SEURAT]: 'Seurat RDS',
-  [sampleFileType.SINGLE_CELL_EXPERIMENT]: 'SingleCellExperiment RDS',
+  [sampleFileType.SEURAT_OBJECT]: 'Seurat RDS',
+  [sampleFileType.SCE_OBJECT]: 'SingleCellExperiment RDS',
   [sampleFileType.FEATURES_PARSE]: 'all_genes.csv',
   [sampleFileType.BARCODES_PARSE]: 'cell_metadata.csv',
   [sampleFileType.MATRIX_PARSE]: 'count_matrix.mtx',
diff --git a/src/utils/upload/fileUploadUtils.js b/src/utils/upload/fileUploadUtils.js
index 9613df5743..bf182de3f6 100644
--- a/src/utils/upload/fileUploadUtils.js
+++ b/src/utils/upload/fileUploadUtils.js
@@ -9,8 +9,8 @@ import { fileObjectToFileRecord } from 'utils/upload/processSampleUpload';
 const techNamesToDisplay = {
   [sampleTech['10X']]: '10X Chromium',
   [sampleTech.RHAPSODY]: 'BD Rhapsody',
-  [sampleTech.SEURAT]: 'Seurat',
-  [sampleTech.SINGLE_CELL_EXPERIMENT]: 'SingleCellExperiment',
+  [sampleTech.SEURAT_OBJECT]: 'Seurat',
+  [sampleTech.SCE_OBJECT]: 'SingleCellExperiment',
   [sampleTech.H5]: '10X Chromium - H5',
   [sampleTech.PARSE]: 'Parse Evercode WT',
 };
@@ -112,7 +112,7 @@ const fileUploadUtils = {
     getFileSampleAndName: getFileSampleAndNameDefault,
     getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech['10X']),
   },
-  [sampleTech.SEURAT]: {
+  [sampleTech.SEURAT_OBJECT]: {
     validExtensionTypes: ['.rds'],
     inputInfo: [
       ['<code>scdata$samples</code>: sample assignment. If absent, treated as unisample.'],
@@ -123,7 +123,7 @@ const fileUploadUtils = {
       ['\uD83D\uDCA1sample level metadata in <code>scdata@meta.data</code> that groups samples in <code>scdata$samples</code> is auto-detected for downstream analysis.'],
       ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'],
     ],
-    requiredFiles: ['seurat'],
+    requiredFiles: [sampleFileType.SEURAT_OBJECT],
     fileUploadParagraphs: [
       '<p>For your dataset, upload a single <code>*.rds</code> file with the Seurat object (max 15GB).</p>',
       '<p>The Seurat object must contain the following slots and metadata:</p>',
@@ -136,13 +136,13 @@ const fileUploadUtils = {
         (validExtension) => fileName.endsWith(validExtension),
       );
     },
-    getCorrespondingType: () => 'seurat',
+    getCorrespondingType: () => sampleFileType.SEURAT_OBJECT,
     // For more information on this one check the TODO1 at FileUploadModal
     filterFiles: () => { throw new Error('Not Implemented'); },
-    getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech.SEURAT),
+    getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech.SEURAT_OBJECT),
     getFileSampleAndName: getFileSampleAndNameDefault,
   },
-  [sampleTech.SINGLE_CELL_EXPERIMENT]: {
+  [sampleTech.SCE_OBJECT]: {
     validExtensionTypes: ['.rds'],
     inputInfo: [
       ['<code>scdata$samples</code>: sample assignment. If absent, treated as unisample.'],
@@ -153,7 +153,7 @@ const fileUploadUtils = {
       ['\uD83D\uDCA1sample level metadata in <code>scdata@meta.data</code> that groups samples in <code>scdata$samples</code> is auto-detected for downstream analysis.'],
       ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'],
     ],
-    requiredFiles: ['single_cell_experiment'],
+    requiredFiles: [sampleFileType.SCE_OBJECT],
     fileUploadParagraphs: [
       '<p>For your dataset, upload a single <code>*.rds</code> file with the SingleCellExperiment object (max 15GB).</p>',
       '<p>The SingleCellExperiment object must contain the following slots and metadata:</p>',
@@ -166,10 +166,10 @@ const fileUploadUtils = {
         (validExtension) => fileName.endsWith(validExtension),
       );
     },
-    getCorrespondingType: () => 'single_cell_experiment',
+    getCorrespondingType: () => sampleFileType.SCE_OBJECT,
     // For more information on this one check the TODO1 at FileUploadModal
     filterFiles: () => { throw new Error('Not Implemented'); },
-    getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech.SINGLE_CELL_EXPERIMENT),
+    getFilePathToDisplay: getFilePathToDisplayDefaultConstructor(sampleTech.SCE_OBJECT),
     getFileSampleAndName: getFileSampleAndNameDefault,
   },
   [sampleTech.RHAPSODY]: {
diff --git a/src/utils/upload/sampleValidators.js b/src/utils/upload/sampleValidators.js
index b679f1a313..c3c5d9abdf 100644
--- a/src/utils/upload/sampleValidators.js
+++ b/src/utils/upload/sampleValidators.js
@@ -9,8 +9,8 @@ import validateParse from 'utils/upload/validateParse';
 const sampleValidators = {
   [sampleTech['10X']]: validate10x,
   [sampleTech.RHAPSODY]: validateRhapsody,
-  [sampleTech.SEURAT]: validateObj2s,
-  [sampleTech.SINGLE_CELL_EXPERIMENT]: validateObj2s,
+  [sampleTech.SEURAT_OBJECT]: validateObj2s,
+  [sampleTech.SCE_OBJECT]: validateObj2s,
   [sampleTech.H5]: validateH5,
   [sampleTech.PARSE]: validateParse,
 };

From 0f0f057cccb194690636f7c44648f1baa0a50fce Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Tue, 17 Sep 2024 15:27:04 -0700
Subject: [PATCH 5/7] update sce modal info

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 src/utils/upload/fileUploadUtils.js | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/utils/upload/fileUploadUtils.js b/src/utils/upload/fileUploadUtils.js
index bf182de3f6..5ed7302089 100644
--- a/src/utils/upload/fileUploadUtils.js
+++ b/src/utils/upload/fileUploadUtils.js
@@ -118,7 +118,7 @@ const fileUploadUtils = {
       ['<code>scdata$samples</code>: sample assignment. If absent, treated as unisample.'],
       ['<code>scdata[[\'RNA\']]@counts</code>: raw feature counts.'],
       ['<code>scdata@reductions</code>: includes a <code>pca</code> reduction.'],
-      ['<code>DefaultDimReduc(scdata)</code>: includes either <code>umap</code> or <code>tsne</code> (e.g. <code>ref.umap</code> will work).'],
+      ['<code>DefaultDimReduc(scdata)</code>: is either <code>umap</code>, <code>tsne</code>, or a close match (e.g. <code>ref.umap</code>).'],
       ['\uD83D\uDCA1cluster metadata in <code>scdata@meta.data</code> is auto-detected.'],
       ['\uD83D\uDCA1sample level metadata in <code>scdata@meta.data</code> that groups samples in <code>scdata$samples</code> is auto-detected for downstream analysis.'],
       ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'],
@@ -145,13 +145,13 @@ const fileUploadUtils = {
   [sampleTech.SCE_OBJECT]: {
     validExtensionTypes: ['.rds'],
     inputInfo: [
-      ['<code>scdata$samples</code>: sample assignment. If absent, treated as unisample.'],
-      ['<code>scdata[[\'RNA\']]@counts</code>: raw feature counts.'],
-      ['<code>scdata@reductions</code>: includes a <code>pca</code> reduction.'],
-      ['<code>DefaultDimReduc(scdata)</code>: includes either <code>umap</code> or <code>tsne</code> (e.g. <code>ref.umap</code> will work).'],
-      ['\uD83D\uDCA1cluster metadata in <code>scdata@meta.data</code> is auto-detected.'],
-      ['\uD83D\uDCA1sample level metadata in <code>scdata@meta.data</code> that groups samples in <code>scdata$samples</code> is auto-detected for downstream analysis.'],
-      ['\uD83D\uDCA1if file size is over 15GB, try removing any assays not indicated above.'],
+      ['<code>sce$samples</code>: sample assignment. If absent, treated as unisample.'],
+      ['<code>counts(sce)</code>: raw feature counts.'],
+      ['<code>reducedDims(sce)</code>: includes a <code>PCA</code> reduction.'],
+      ['<code>reducedDimNames(sce)</code>: includes either <code>UMAP</code>, <code>TSNE</code>, or a close match (e.g. <code>REF.UMAP</code>).'],
+      ['\uD83D\uDCA1cluster metadata in <code>sce@colData</code> is auto-detected.'],
+      ['\uD83D\uDCA1sample level metadata in <code>sce@colData</code> that groups samples in <code>sce$samples</code> is auto-detected for downstream analysis.'],
+      ['\uD83D\uDCA1if file size is over 15GB, try removing any slots not indicated above.'],
     ],
     requiredFiles: [sampleFileType.SCE_OBJECT],
     fileUploadParagraphs: [

From 303b787063a75a0122b1ecf356eabe26b2f3e9dd Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Tue, 17 Sep 2024 15:36:07 -0700
Subject: [PATCH 6/7] generalize obj2s user messages

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 src/utils/pipelineErrorUserMessages.js | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/utils/pipelineErrorUserMessages.js b/src/utils/pipelineErrorUserMessages.js
index 3f9f35053e..4fb0b7ec2c 100644
--- a/src/utils/pipelineErrorUserMessages.js
+++ b/src/utils/pipelineErrorUserMessages.js
@@ -1,9 +1,9 @@
 export default {
-  ERROR_SEURAT_RDS: '\u26A0\uFE0F We couldn\'t read the uploaded rds file. Please check requirements and re-upload after fixing.',
-  ERROR_SEURAT_COUNTS: '\u26A0\uFE0F We couldn\'t get the `counts` slot from the `RNA` assay of the uploaded Seurat object. Please check requirements and re-upload after fixing.',
-  ERROR_SEURAT_HVFINFO: '\u26A0\uFE0F We couldn\'t run `FindVariableFeatures` on the `data` slot from the `RNA` assay of the uploaded Seurat object. Please check requirements and re-upload after fixing.',
-  ERROR_SEURAT_METADATA: '\u26A0\uFE0F We couldn\'t get the `meta.data` slot from the uploaded Seurat object. Please check requirements and re-upload after fixing.',
-  ERROR_SEURAT_CLUSTERS: '\u26A0\uFE0F We couldn\'t detect clusters in the `meta.data` slot from the uploaded Seurat object. Please check requirements and re-upload after fixing.',
-  ERROR_SEURAT_REDUCTION: '\u26A0\uFE0F We couldn\'t get the `pca` and `umap` or `tsne` dimensionality reduction from the uploaded Seurat object. Please check requirements and re-upload after fixing.',
-  ERROR_SEURAT_LOGCOUNTS: '\u26A0\uFE0F We couldn\'t get the `data` slot from the `RNA` assay of the uploaded Seurat object. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_RDS: '\u26A0\uFE0F We couldn\'t read the uploaded file. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_COUNTS: '\u26A0\uFE0F We couldn\'t get the feature counts from the uploaded object. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_HVFINFO: '\u26A0\uFE0F We couldn\'t run `FindVariableFeatures` on the logcounts from the uploaded object. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_METADATA: '\u26A0\uFE0F We couldn\'t get the meta data from the uploaded object. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_CLUSTERS: '\u26A0\uFE0F We couldn\'t detect clusters in the metadata from the uploaded object. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_REDUCTION: '\u26A0\uFE0F We couldn\'t get the PCA and UMAP or TSNE dimensionality reduction from the uploaded object. Please check requirements and re-upload after fixing.',
+  ERROR_OBJ2S_LOGCOUNTS: '\u26A0\uFE0F We couldn\'t get the logcounts from the uploaded object. Please check requirements and re-upload after fixing.',
 };

From ab857488a97d9d34e5ffd103733df4406882f8f4 Mon Sep 17 00:00:00 2001
From: Alex Pickering <alexvpickering@gmail.com>
Date: Wed, 18 Sep 2024 15:25:05 -0700
Subject: [PATCH 7/7] adjust modal tests for obj2s types

Signed-off-by: Alex Pickering <alexvpickering@gmail.com>
---
 .../data-management/FileUploadModal.test.jsx  | 141 ++++++++++++++----
 1 file changed, 108 insertions(+), 33 deletions(-)

diff --git a/src/__test__/components/data-management/FileUploadModal.test.jsx b/src/__test__/components/data-management/FileUploadModal.test.jsx
index 62e223be85..e3dfce70f0 100644
--- a/src/__test__/components/data-management/FileUploadModal.test.jsx
+++ b/src/__test__/components/data-management/FileUploadModal.test.jsx
@@ -12,7 +12,7 @@ import handleError from 'utils/http/handleError';
 import endUserMessages from 'utils/endUserMessages';
 
 import techOptions, { techNamesToDisplay } from 'utils/upload/fileUploadUtils';
-import { sampleTech } from 'utils/constants';
+import { sampleTech, obj2sTechs } from 'utils/constants';
 
 import mockFile from '__test__/test-utils/mockFile';
 import FileUploadModal from 'components/data-management/FileUploadModal';
@@ -119,7 +119,7 @@ describe('FileUploadModal', () => {
     expect(uploadInput.getAttribute('webkitdirectory')).toBe('');
   });
 
-  it('contains required components for Seurat', async () => {
+  it('contains required components for Seurat object uploads', async () => {
     await renderFileUploadModal(initialStore);
 
     // It has default 10x selected
@@ -164,6 +164,50 @@ describe('FileUploadModal', () => {
     expect(uploadButton).toBeDisabled();
   });
 
+  it('contains required components for SingleCellExperiment object uploads', async () => {
+    await renderFileUploadModal(initialStore);
+
+    // It has default 10x selected
+    expect(screen.queryAllByText(techNamesToDisplay[sampleTech['10X']]).length).toBe(1);
+
+    selectTech(sampleTech.SCE_OBJECT);
+
+    // Lists the requirements of the Seurat object
+    expect(screen.getByText(/The SingleCellExperiment object must contain the following slots and metadata:/i)).toBeInTheDocument();
+
+    // samples
+    expect(screen.getAllByText(/sce\$samples/i).length).toBe(2);
+
+    // counts
+    expect(screen.getByText(/counts\(sce\)/i)).toBeInTheDocument();
+
+    // reductions
+    expect(screen.getByText(/reducedDimNames\(sce\)/i)).toBeInTheDocument();
+
+    // inform users that cluster metadata is auto-detected
+    expect(screen.getByText(/cluster metadata .+ is auto-detected/i)).toBeInTheDocument();
+
+    // inform users that sample level metadata is auto-detected
+    expect(screen.getByText(/sample level metadata .+ is auto-detected/i)).toBeInTheDocument();
+
+    // told to drag and drop rds file
+    expect(screen.getByText(/Drag and drop \*\.rds file here or click to browse\./i)).toBeInTheDocument();
+
+    // if click to browse will be able to upload file instead of folder
+    const uploadInput = document.querySelector(
+      `[data-test-id="${integrationTestConstants.ids.FILE_UPLOAD_INPUT}"]`,
+    );
+
+    expect(uploadInput.getAttribute('webkitdirectory')).toBe(null);
+
+    // It has a disabled upload button if there are no uploaded files
+    // Upload button is the last "Upload" text in the document
+    const uploadButtonText = screen.getAllByText(/Upload/i).pop();
+    const uploadButton = uploadButtonText.closest('button');
+
+    expect(uploadButton).toBeDisabled();
+  });
+
   it('drag and drop works with valid 10X Chromium file', async () => {
     await renderFileUploadModal(initialStore);
 
@@ -200,10 +244,10 @@ describe('FileUploadModal', () => {
     expect(uploadButton).not.toBeDisabled();
   });
 
-  it('drag and drop works with valid Seurat file', async () => {
+  test.each(obj2sTechs)('drag and drop works with valid Obj2s files for tech %s', async (obj2sTech) => {
     await renderFileUploadModal(initialStore);
 
-    selectTech(sampleTech.SEURAT_OBJECT);
+    selectTech(obj2sTech);
 
     expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
 
@@ -212,10 +256,10 @@ describe('FileUploadModal', () => {
       `[data-test-id="${integrationTestConstants.ids.FILE_UPLOAD_INPUT}"]`,
     );
 
-    // create a seurat file
+    // create a file specific to each tech if needed
     const file = mockFile('scdata.rds');
 
-    //  drop it into drop-zone
+    // drop it into drop-zone
     await act(async () => {
       Object.defineProperty(uploadInput, 'files', {
         value: [file],
@@ -224,23 +268,56 @@ describe('FileUploadModal', () => {
       fireEvent.drop(uploadInput);
     });
 
-    //  it was valid and shows up
+    // it was valid and shows up
     expect(await screen.findByText(/To upload/)).toBeInTheDocument();
     expect(await screen.findByText('scdata.rds')).toBeInTheDocument();
 
     // upload is enabled
-    // It has a disabled upload button if there are no uploaded files
-    // Upload button is the last "Upload" text in the document
     const uploadButtonText = screen.getAllByText(/Upload/i).pop();
     const uploadButton = uploadButtonText.closest('button');
 
     expect(uploadButton).not.toBeDisabled();
   });
 
-  it('drag and drop works with valid Seurat file when different experiment has valid uploaded Seurat object', async () => {
+  test.each(obj2sTechs)('drag and drop works with valid Obj2s files for tech %s', async (obj2sTech) => {
+    await renderFileUploadModal(initialStore);
+
+    selectTech(obj2sTech);
+
+    expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
+
+    // get the dropzone input
+    const uploadInput = document.querySelector(
+      `[data-test-id="${integrationTestConstants.ids.FILE_UPLOAD_INPUT}"]`,
+    );
+
+    // create a mock file with a fixed name 'scdata.rds'
+    const file = mockFile('scdata.rds');
+
+    // drop the file into the drop-zone
+    await act(async () => {
+      Object.defineProperty(uploadInput, 'files', {
+        value: [file],
+      });
+
+      fireEvent.drop(uploadInput);
+    });
+
+    // expect the file to appear as uploaded
+    expect(await screen.findByText(/To upload/)).toBeInTheDocument();
+    expect(await screen.findByText('scdata.rds')).toBeInTheDocument();
+
+    // check that the upload button is enabled
+    const uploadButtonText = screen.getAllByText(/Upload/i).pop();
+    const uploadButton = uploadButtonText.closest('button');
+
+    expect(uploadButton).not.toBeDisabled();
+  });
+
+  test.each(obj2sTechs)('drag and drop works with valid Seurat file when different experiment has valid uploaded Obj2s file for tech %s', async (obj2sTech) => {
     await renderFileUploadModal(prevUpDiffExpStore);
 
-    selectTech(sampleTech.SEURAT_OBJECT);
+    selectTech(obj2sTech);
 
     expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
 
@@ -249,10 +326,10 @@ describe('FileUploadModal', () => {
       `[data-test-id="${integrationTestConstants.ids.FILE_UPLOAD_INPUT}"]`,
     );
 
-    // create a seurat file
+    // create a mock file with a fixed name 'scdata.rds'
     const file = mockFile('scdata.rds');
 
-    //  drop it into drop-zone
+    // drop the file into the drop-zone
     await act(async () => {
       Object.defineProperty(uploadInput, 'files', {
         value: [file],
@@ -261,20 +338,18 @@ describe('FileUploadModal', () => {
       fireEvent.drop(uploadInput);
     });
 
-    //  it was valid and shows up
+    // expect the file to appear as uploaded
     expect(await screen.findByText(/To upload/)).toBeInTheDocument();
     expect(await screen.findByText('scdata.rds')).toBeInTheDocument();
 
-    // upload is enabled
-    // It has a disabled upload button if there are no uploaded files
-    // Upload button is the last "Upload" text in the document
+    // check that the upload button is enabled
     const uploadButtonText = screen.getAllByText(/Upload/i).pop();
     const uploadButton = uploadButtonText.closest('button');
 
     expect(uploadButton).not.toBeDisabled();
   });
 
-  it('drag and drop does not work with invalid Seurat file', async () => {
+  test.each(obj2sTechs)('drag and drop does not work with invalid Obj2s file for tech %s', async (obj2sTech) => {
     await renderFileUploadModal(initialStore);
 
     // technology input should be enabled because there is no previously uploaded data
@@ -284,7 +359,7 @@ describe('FileUploadModal', () => {
 
     expect(techInput).toBeEnabled();
 
-    selectTech(sampleTech.SEURAT_OBJECT);
+    selectTech(obj2sTech);
 
     expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();
 
@@ -293,10 +368,10 @@ describe('FileUploadModal', () => {
       `[data-test-id="${integrationTestConstants.ids.FILE_UPLOAD_INPUT}"]`,
     );
 
-    // create a seurat file
+    // create an invalid file
     const file = mockFile('scdata.txt');
 
-    //  drop it into drop-zone
+    // drop the invalid file into the drop-zone
     await act(async () => {
       Object.defineProperty(uploadInput, 'files', {
         value: [file],
@@ -305,26 +380,26 @@ describe('FileUploadModal', () => {
       fireEvent.drop(uploadInput);
     });
 
-    //  it shows up
+    // expect the invalid file to show up
     expect(await screen.findByText(/To upload/)).toBeInTheDocument();
     expect(await screen.findByText('scdata.txt')).toBeInTheDocument();
 
-    // upload is disabled as the file was invalid
+    // check that the upload button is disabled as the file is invalid
     const uploadButtonText = screen.getAllByText(/Upload/i).pop();
     const uploadButton = uploadButtonText.closest('button');
 
     expect(uploadButton).toBeDisabled();
   });
 
-  it('drag and drop fails with valid Seurat file when pre-existing Seurat file exists for experiment', async () => {
-    await renderFileUploadModal(prevUpStore, sampleTech.SEURAT_OBJECT);
+  test.each(obj2sTechs)('drag and drop fails with valid Obj2s file when pre-existing Obj2s file exists for experiment for tech %s', async (obj2sTech) => {
+    await renderFileUploadModal(prevUpStore, obj2sTech);
 
-    // Seurat info should show up as their is previous Seurat data uploaded
+    // relevant tech info should show up as there is previously uploaded data
     await waitFor(() => expect(
-      screen.getByText(/Seurat object \(max 15GB\)/),
+      screen.getByText(/object must contain the following slots and metadata/),
     ).toBeInTheDocument());
 
-    // technology input should be disable because we have existing data
+    // technology input should be disabled because we have existing data
     const techInput = document.querySelector(
       '[data-testid="uploadTechSelect"] input',
     );
@@ -338,10 +413,10 @@ describe('FileUploadModal', () => {
       `[data-test-id="${integrationTestConstants.ids.FILE_UPLOAD_INPUT}"]`,
     );
 
-    // create a seurat file
+    // create a valid file
     const file = mockFile('scdata.rds');
 
-    //  drop it into drop-zone
+    // drop the valid file into the drop-zone
     await act(async () => {
       Object.defineProperty(uploadInput, 'files', {
         value: [file],
@@ -350,16 +425,16 @@ describe('FileUploadModal', () => {
       fireEvent.drop(uploadInput);
     });
 
-    //  it was not valid and doesn't shows up
+    // expect that the file does not show up due to pre-existing file
     expect(await screen.queryByText('scdata.rds')).not.toBeInTheDocument();
 
-    // upload is disabled as there is pre-existing file for experiment
+    // upload should be disabled as a pre-existing file exists for the experiment
     const uploadButtonText = screen.getAllByText(/Upload/i).pop();
     const uploadButton = uploadButtonText.closest('button');
 
     expect(uploadButton).toBeDisabled();
 
-    // error message was displayed to user
+    // expect an error message to be displayed to the user
     expect(handleError).toHaveBeenCalledWith('error', endUserMessages.ERROR_OBJ2S_EXISTING_FILE);
   });