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Merge pull request #1000 from hms-dbmi-cellenics/add-sce-upload
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init sce upload; rename seurat pipeline to obj2s
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@alexvpickering
alexvpickering authored Sep 19, 2024
2 parents de7ddd6 + ab85748 commit e9b234e
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Showing 37 changed files with 381 additions and 266 deletions.
2 changes: 1 addition & 1 deletion src/__test__/components/ContentWrapper.test.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ describe('ContentWrapper', () => {
status: 'SUCCEEDED',
shouldRerun: false,
},
seurat: {
obj2s: {
status: 'NOT_CREATED',
},
},
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2 changes: 1 addition & 1 deletion src/__test__/components/data-management/DownloadDataButton.test.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -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 () => {
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147 changes: 111 additions & 36 deletions src/__test__/components/data-management/FileUploadModal.test.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -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';
Expand Down Expand Up @@ -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];
Expand Down Expand Up @@ -119,14 +119,14 @@ 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
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();
Expand Down Expand Up @@ -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);

Expand Down Expand Up @@ -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);
selectTech(obj2sTech);

expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();

Expand All @@ -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],
Expand All @@ -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);
selectTech(obj2sTech);

expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();

Expand All @@ -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],
Expand All @@ -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
Expand All @@ -284,7 +359,7 @@ describe('FileUploadModal', () => {

expect(techInput).toBeEnabled();

selectTech(sampleTech.SEURAT);
selectTech(obj2sTech);

expect(await screen.queryByText(/To upload/)).not.toBeInTheDocument();

Expand All @@ -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],
Expand All @@ -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);
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',
);
Expand All @@ -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],
Expand All @@ -350,17 +425,17 @@ 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(handleError).toHaveBeenCalledWith('error', endUserMessages.ERROR_SEURAT_EXISTING_FILE);
// expect an error message to be displayed to the user
expect(handleError).toHaveBeenCalledWith('error', endUserMessages.ERROR_OBJ2S_EXISTING_FILE);
});

it('Shows what files can be uploaded for Rhapsody samples', async () => {
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