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[ENH] Standardized query result files #392

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merged 6 commits into from
Dec 12, 2024
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Merged

[ENH] Standardized query result files #392

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2e5d722
Revert "Updated the `ResultsTSV` e2e test"
rmanaem Dec 5, 2024
7a40a68
Revert "Updated formatting of download result files"
rmanaem Dec 5, 2024
9414b43
Bump eslint-plugin-react-refresh from 0.4.14 to 0.4.16 (#394)
dependabot[bot] Dec 9, 2024
8b29587
Bump @vitest/ui from 2.1.5 to 2.1.8 (#395)
dependabot[bot] Dec 9, 2024
f3c5210
[FIX] Replaced the latest version tag with a baked-in version (#390)
rmanaem Dec 10, 2024
74187a7
Update CHANGELOG.md [skip ci]
Dec 10, 2024
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22 changes: 11 additions & 11 deletions cypress/e2e/ResultsTSV.cy.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ describe('Results TSV', () => {
});
});
describe('Unprotected response', () => {
it.only('Checks whether the rows in the participant.tsv file generated according to session_type', () => {
it('Checks whether the rows in the participant.tsv file generated according to session_type', () => {
cy.intercept('query?*', unprotectedResponse).as('call');
cy.intercept(
{
Expand Down Expand Up @@ -107,12 +107,12 @@ describe('Unprotected response', () => {
expect(phenotypicSession.split('\t')[4]).to.equal('ses-nb01');
expect(phenotypicSession.split('\t')[5]).to.equal('');
expect(phenotypicSession.split('\t')[6]).to.equal('Phenotypic');
expect(phenotypicSession.split('\t')[7]).to.equal('1');
expect(phenotypicSession.split('\t')[8]).to.equal('0');
expect(phenotypicSession.split('\t')[9]).to.equal('10.4');
expect(phenotypicSession.split('\t')[10]).to.equal('female');
expect(phenotypicSession.split('\t')[11]).to.equal('Major depressive disorder');
expect(phenotypicSession.split('\t')[12]).to.equal('multisource interference task');
expect(phenotypicSession.split('\t')[7]).to.equal('10.4');
expect(phenotypicSession.split('\t')[8]).to.equal('female');
expect(phenotypicSession.split('\t')[9]).to.equal('Major depressive disorder');
expect(phenotypicSession.split('\t')[10]).to.equal('multisource interference task');
expect(phenotypicSession.split('\t')[11]).to.equal('1');
expect(phenotypicSession.split('\t')[12]).to.equal('0');
expect(phenotypicSession.split('\t')[13]).to.equal('');
expect(phenotypicSession.split('\t')[14]).to.equal('');
expect(phenotypicSession.split('\t')[15]).to.equal('Flow Weighted, T2 Weighted');
Expand All @@ -127,12 +127,12 @@ describe('Unprotected response', () => {
expect(imagingSession.split('\t')[4]).to.equal('ses-nb01');
expect(imagingSession.split('\t')[5]).to.equal('/ds004116/sub-300101');
expect(imagingSession.split('\t')[6]).to.equal('Imaging');
expect(imagingSession.split('\t')[7]).to.equal('0');
expect(imagingSession.split('\t')[8]).to.equal('1');
expect(imagingSession.split('\t')[7]).to.equal('');
expect(imagingSession.split('\t')[8]).to.equal('');
expect(imagingSession.split('\t')[9]).to.equal('');
expect(imagingSession.split('\t')[10]).to.equal('');
expect(imagingSession.split('\t')[11]).to.equal('');
expect(imagingSession.split('\t')[12]).to.equal('');
expect(imagingSession.split('\t')[11]).to.equal('0');
expect(imagingSession.split('\t')[12]).to.equal('1');
expect(imagingSession.split('\t')[13]).to.equal('Flow Weighted, T2 Weighted');
expect(imagingSession.split('\t')[14]).to.equal('fmriprep 23.1.3, freesurfer 7.3.2');
expect(imagingSession.split('\t')[15]).to.equal('Flow Weighted, T2 Weighted');
Expand Down
220 changes: 131 additions & 89 deletions src/components/ResultContainer.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -145,104 +145,146 @@ function ResultContainer({
const tsvRows = [];
const datasets = response.responses.filter((res) => download.includes(res.dataset_uuid));

const isHumanFile = buttonIdentifier === 'cohort-participant';
if (buttonIdentifier === 'cohort-participant') {
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issue (complexity): Consider extracting the export logic into a reusable configuration-driven function.

The export logic can be simplified by extracting the common pattern into a reusable function. Here's how:

interface FieldConfig {
  header: string;
  getValue: (res: any, subject?: any) => string;
  protected?: string;
}

const exportConfigs = {
  'cohort-participant': {
    fields: [
      { header: 'DatasetName', getValue: (res) => res.dataset_name.replace('\n', ' ') },
      { header: 'SubjectID', getValue: (_, subject) => subject?.sub_id, protected: 'protected' },
      // ... other fields
    ]
  },
  'other-export': {
    fields: [
      // ... field configurations
    ]
  }
};

function generateTSVString(buttonIdentifier: string) {
  if (!response) return '';

  const config = exportConfigs[buttonIdentifier];
  const datasets = response.responses.filter((res) => download.includes(res.dataset_uuid));
  const tsvRows = [config.fields.map(f => f.header).join('\t')];

  datasets.forEach(res => {
    if (res.records_protected) {
      tsvRows.push(config.fields.map(f => f.protected || 'protected').join('\t'));
    } else {
      res.subject_data.forEach(subject => {
        tsvRows.push(config.fields.map(f => f.getValue(res, subject)).join('\t'));
      });
    }
  });

  return tsvRows.join('\n');
}

This approach:

  • Eliminates code duplication
  • Makes field definitions and differences between export types explicit
  • Easier to maintain and extend with new export types
  • Reduces chance of bugs when making changes

const headers = [
'DatasetName',
'PortalURI',
'NumMatchingSubjects',
'SubjectID',
'SessionID',
'SessionFilePath',
'SessionType',
'Age',
'Sex',
'Diagnosis',
'Assessment',
'NumMatchingPhenotypicSessions',
'NumMatchingImagingSessions',
'SessionImagingModalities',
'SessionCompletedPipelines',
'DatasetImagingModalities',
'DatasetPipelines',
].join('\t');
tsvRows.push(headers);

const headers = [
'DatasetName',
'PortalURI',
'NumMatchingSubjects',
'SubjectID',
'SessionID',
'ImagingSessionPath',
'SessionType',
'NumMatchingPhenotypicSessions',
'NumMatchingImagingSessions',
'Age',
'Sex',
'Diagnosis',
'Assessment',
'SessionImagingModalities',
'SessionCompletedPipelines',
'DatasetImagingModalities',
'DatasetPipelines',
].join('\t');
tsvRows.push(headers);

datasets.forEach((res) => {
if (res.records_protected) {
tsvRows.push(
[
res.dataset_name.replace('\n', ' '),
res.dataset_portal_uri,
res.num_matching_subjects,
'protected', // subject_id
'protected', // session_id
'protected', // session_file_path
'protected', // session_type
'protected', // num_matching_phenotypic_sessions
'protected', // num_matching_imaging_sessions
'protected', // age
'protected', // sex
'protected', // diagnosis
'protected', // assessment
'protected', // session_imaging_modality
'protected', // session_completed_pipelines
isHumanFile
? convertURIToLabel('modality', res.image_modals)
: res.image_modals?.join(', '),
isHumanFile
? convertURIToLabel(
datasets.forEach((res) => {
if (res.records_protected) {
tsvRows.push(
[
res.dataset_name.replace('\n', ' '),
res.dataset_portal_uri,
res.num_matching_subjects,
'protected', // subject_id
'protected', // session_id
'protected', // session_file_path
'protected', // session_type
'protected', // age
'protected', // sex
'protected', // diagnosis
'protected', // assessment
'protected', // num_matching_phenotypic_sessions
'protected', // num_matching_imaging_sessions
'protected', // session_imaging_modality
'protected', // session_completed_pipelines
convertURIToLabel('modality', res.image_modals),
convertURIToLabel(
'pipeline',
parsePipelinesInfoToString(res.available_pipelines).split(', ')
),
].join('\t')
);
} else {
// @ts-expect-error: typescript doesn't know that subject_data is an array when records_protected is false.
res.subject_data.forEach((subject) => {
tsvRows.push(
[
res.dataset_name.replace('\n', ' '),
res.dataset_portal_uri,
res.num_matching_subjects,
subject.sub_id,
subject.session_id,
subject.session_file_path,
convertURIToLabel('sessionType', subject.session_type),
subject.age,
convertURIToLabel('sex', subject.sex),
convertURIToLabel('diagnosis', subject.diagnosis),
convertURIToLabel('assessment', subject.assessment),
subject.num_matching_phenotypic_sessions,
subject.num_matching_imaging_sessions,
convertURIToLabel('modality', subject.image_modal),
convertURIToLabel(
'pipeline',
parsePipelinesInfoToString(subject.completed_pipelines).split(', ')
),
convertURIToLabel('modality', res.image_modals),
convertURIToLabel(
'pipeline',
parsePipelinesInfoToString(res.available_pipelines).split(', ')
)
: parsePipelinesInfoToString(res.available_pipelines),
].join('\t')
);
} else {
// @ts-expect-error: typescript doesn't know that subject_data is an array when records_protected is false.
res.subject_data.forEach((subject) => {
),
].join('\t')
);
});
}
});
} else {
const headers = [
'DatasetName',
'PortalURI',
'SubjectID',
'SessionID',
'SessionFilePath',
'SessionType',
'NumMatchingPhenotypicSessions',
'NumMatchingImagingSessions',
'SessionImagingModalities',
'SessionCompletedPipelines',
'DatasetImagingModalities',
'DatasetPipelines',
].join('\t');
tsvRows.push(headers);

datasets.forEach((res) => {
if (res.records_protected) {
tsvRows.push(
[
res.dataset_name.replace('\n', ' '),
res.dataset_portal_uri,
res.num_matching_subjects,
subject.sub_id,
subject.session_id,
subject.session_file_path,
isHumanFile
? convertURIToLabel('sessionType', subject.session_type)
: subject.session_type,
subject.num_matching_phenotypic_sessions,
subject.num_matching_imaging_sessions,
subject.age,
isHumanFile ? convertURIToLabel('sex', subject.sex) : subject.sex,
isHumanFile ? convertURIToLabel('diagnosis', subject.diagnosis) : subject.diagnosis,
isHumanFile
? convertURIToLabel('assessment', subject.assessment)
: subject.assessment,
isHumanFile
? convertURIToLabel('modality', subject.image_modal)
: subject.image_modal?.join(', '),
isHumanFile
? convertURIToLabel(
'pipeline',
parsePipelinesInfoToString(subject.completed_pipelines).split(', ')
)
: parsePipelinesInfoToString(subject.completed_pipelines),
isHumanFile
? convertURIToLabel('modality', res.image_modals)
: res.image_modals?.join(', '),
isHumanFile
? convertURIToLabel(
'pipeline',
parsePipelinesInfoToString(res.available_pipelines).split(', ')
)
: parsePipelinesInfoToString(res.available_pipelines),
'protected', // subject_id
'protected', // session_id
'protected', // session_file_path
'protected', // session_type
'protected', // num_matching_phenotypic_sessions
'protected', // num_matching_imaging_sessions
'protected', // session_imaging_modality
'protected', // session_completed_pipelines
res.image_modals?.join(', '),
parsePipelinesInfoToString(res.available_pipelines),
].join('\t')
);
});
}
});
} else {
// @ts-expect-error: typescript doesn't know that subject_data is an array when records_protected is false.
res.subject_data.forEach((subject) => {
tsvRows.push(
[
res.dataset_name.replace('\n', ' '),
res.dataset_portal_uri,
subject.sub_id,
subject.session_id,
subject.session_file_path,
subject.session_type,
subject.num_matching_phenotypic_sessions,
subject.num_matching_imaging_sessions,
subject.image_modal?.join(', '),
parsePipelinesInfoToString(subject.completed_pipelines),
res.image_modals?.join(', '),
parsePipelinesInfoToString(res.available_pipelines),
].join('\t')
);
});
}
});
}

return tsvRows.join('\n');
}

Expand Down
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