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[VISIUM EXAMPLE] disable file check #570

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[VISIUM EXAMPLE] disable file check #570

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eb91056
disable file check
alexvpickering Nov 30, 2021
23e16fd
disable tests
alexvpickering Nov 30, 2021
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120 changes: 60 additions & 60 deletions src/__test__/components/data-management/LaunchAnalysisButton.test.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -161,66 +161,66 @@ describe('LaunchAnalysisButton', () => {
jest.clearAllMocks();
});

it('Process project button is disabled if not all sample metadata are inserted', () => {
const notAllMetadataInserted = {
...withDataState,
samples: {
...withDataState.samples,
[sample1Uuid]: {
...withDataState.samples[sample1Uuid],
metadata: [''],
},
},
};

render(
<Provider store={mockStore(notAllMetadataInserted)}>
<LaunchAnalysisButton />
</Provider>,
);

const button = screen.getByText('Process project').closest('button');

expect(button).toBeDisabled();
});

it('Process project button is disabled if there is no data', () => {
render(
<Provider store={mockStore(noDataState)}>
<LaunchAnalysisButton />
</Provider>,
);

const button = screen.getByText('Process project').closest('button');

expect(button).toBeDisabled();
});

it('Process project button is disabled if not all data are uploaded', () => {
const notAllDataUploaded = {
...withDataState,
samples: {
...withDataState.samples,
[sample1Uuid]: {
...withDataState.samples[sample1Uuid],
files: {
...withDataState.samples[sample1Uuid].files,
'features.tsv.gz': { valid: true, upload: { status: UploadStatus.UPLOADING } },
},
},
},
};

render(
<Provider store={mockStore(notAllDataUploaded)}>
<LaunchAnalysisButton />
</Provider>,
);

const button = screen.getByText('Process project').closest('button');

expect(button).toBeDisabled();
});
// it('Process project button is disabled if not all sample metadata are inserted', () => {
// const notAllMetadataInserted = {
// ...withDataState,
// samples: {
// ...withDataState.samples,
// [sample1Uuid]: {
// ...withDataState.samples[sample1Uuid],
// metadata: [''],
// },
// },
// };

// render(
// <Provider store={mockStore(notAllMetadataInserted)}>
// <LaunchAnalysisButton />
// </Provider>,
// );

// const button = screen.getByText('Process project').closest('button');

// expect(button).toBeDisabled();
// });

// it('Process project button is disabled if there is no data', () => {
// render(
// <Provider store={mockStore(noDataState)}>
// <LaunchAnalysisButton />
// </Provider>,
// );

// const button = screen.getByText('Process project').closest('button');

// expect(button).toBeDisabled();
// });

// it('Process project button is disabled if not all data are uploaded', () => {
// const notAllDataUploaded = {
// ...withDataState,
// samples: {
// ...withDataState.samples,
// [sample1Uuid]: {
// ...withDataState.samples[sample1Uuid],
// files: {
// ...withDataState.samples[sample1Uuid].files,
// 'features.tsv.gz': { valid: true, upload: { status: UploadStatus.UPLOADING } },
// },
// },
// },
// };

// render(
// <Provider store={mockStore(notAllDataUploaded)}>
// <LaunchAnalysisButton />
// </Provider>,
// );

// const button = screen.getByText('Process project').closest('button');

// expect(button).toBeDisabled();
// });

it('Process project button is enabled if there is data and all metadata for all samples are uplaoded', () => {
render(
Expand Down
18 changes: 2 additions & 16 deletions src/components/data-management/LaunchAnalysisButton.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -135,8 +135,8 @@ const LaunchAnalysisButton = () => {
for (const fileName of fileNames) {
const checkedFile = sample.files[fileName];
allUploaded = allUploaded
&& checkedFile.valid
&& checkedFile.upload.status === UploadStatus.UPLOADED;
&& checkedFile.valid
&& checkedFile.upload.status === UploadStatus.UPLOADED;

if (!allUploaded) break;
}
Expand Down Expand Up @@ -166,20 +166,6 @@ const LaunchAnalysisButton = () => {
return <LaunchButtonTemplate text='Loading project...' disabled loading />;
}

if (!canLaunchAnalysis()) {
return (
<Tooltip
title='Ensure all samples are uploaded and all metadata are inserted'
>
{/* disabled button inside tooltip causes tooltip to not function */}
{/* https://github.com/react-component/tooltip/issues/18#issuecomment-140078802 */}
<span>
<LaunchButtonTemplate text={buttonText} disabled />
</span>
</Tooltip>
);
}

// Popconfirm
if (gem2sRerunStatus.rerun) {
return (
Expand Down
2 changes: 1 addition & 1 deletion src/utils/upload/fileInspector.js
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Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ const inspectFile = async (file, technology) => {

// check barcodes file starts with a 16 digit DNA sequence
if (file.name.startsWith('barcodes')
&& !data.toString().match(/\t/)) {
&& !data.toString().match(/\t/)) {
return valid;
}

Expand Down
6 changes: 4 additions & 2 deletions src/utils/upload/processUpload.js
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ import fetchAPI from '../fetchAPI';

import UploadStatus from './UploadStatus';
import loadAndCompressIfNecessary from './loadAndCompressIfNecessary';
import { inspectFile, Verdict } from './fileInspector';
import { Verdict } from './fileInspector';

const putInS3 = async (projectUuid, loadedFileData, dispatch, sampleUuid, fileName, metadata) => {
const baseUrl = `/v1/projects/${projectUuid}/samples/${sampleUuid}/${fileName}/uploadUrl`;
Expand Down Expand Up @@ -226,7 +226,9 @@ const bundleToFile = async (bundle, technology) => {
? _.takeRight(bundle.path.split('/'), 2).join('/')
: bundle.name;

const verdict = await inspectFile(bundle, technology);
const verdict = true;
console.log(technology);
// const verdict = await inspectFile(bundle, technology);

let error = '';
if (verdict === Verdict.INVALID_NAME) {
Expand Down