[ENH] Standardized query result files

[rmanaem]

• Closes Standardize query result files #389
• See also [MNT] Updated query-tool-results files neurobagel_examples#47

Checklist

This section is for the PR reviewer

• PR has an interpretable title with a prefix ([ENH], [FIX], [REF], [TST], [CI], [MNT], [INF], [MODEL], [DOC]) (see our Contributing Guidelines for more info)
• PR has a label for the release changelog or skip-release (to be applied by maintainers only)
• PR links to GitHub issue with mention Closes #XXXX
• Tests pass
• Checks pass
• If the PR changes the participant-level and/or the dataset-level result file, the query-tool-results files in the neurobagel_examples repo have been regenerated

For new features:

• Tests have been added

For bug fixes:

• There is at least one test that would fail under the original bug conditions.

Summary by Sourcery

Standardize the format of query result files by updating the headers and data structure for TSV files, and update tests to ensure correct data mapping and validation.

Enhancements:

• Standardize the format of query result files by updating the headers and data structure for TSV files.

Tests:

• Update tests to reflect changes in the TSV file structure, ensuring correct data mapping and validation.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR standardizes the query result files by reorganizing the column order and handling human-readable vs. machine-readable outputs more consistently. The changes primarily focus on the TSV file generation logic in the ResultContainer component and its corresponding tests.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change	Details	Files
Reorganized TSV column structure and separated human-readable vs. machine-readable output handling	Moved demographic columns (Age, Sex, Diagnosis, Assessment) before session count columns Split TSV generation logic into two distinct code paths based on file type Standardized the use of convertURIToLabel for human-readable files Removed redundant conditional checks for human file conversion	src/components/ResultContainer.tsx
Updated test cases to match new column ordering	Updated column index assertions to match new column order Removed .only modifier from test case Adjusted expected values for session counts and demographic data positions	cypress/e2e/ResultsTSV.cy.ts

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#389	Create a file with descriptive human-readable labels	✅
#389	Create a file with URIs (machine-optimized format)	✅

Possibly linked issues

• Standardize query result files #389: The PR implements the standardization of query result files as described in the issue.

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[sourcery-ai]

Hey @rmanaem - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟡 Complexity: 1 issue found
• 🟢 Documentation: all looks good

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[sourcery-ai]

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

[surchs]

Hey @rmanaem I think you have the PR target mixed up here

The diff also looks a little funny. Would you mind checking what is happening here and then let me know?