[ENH] Standardized query result files

[rmanaem]

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

NOTE: If this pull request is to be released, the release label must be applied once the review process is done to avoid the local and remote from going out of sync as a consequence of the bump version workflow run

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 to ensure consistency across different datasets and scenarios, and update tests to validate the new format.

Enhancements:

• Standardize the format of query result files by unifying the headers and data structure for both protected and unprotected records.

Tests:

• Update tests to reflect the new standardized format of query result files, ensuring correct data mapping and validation.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR standardizes the query result files by consolidating the logic for both human-readable and machine-readable formats into a single code path. The changes reorganize the column order in the TSV output and introduce conditional formatting based on the file type.

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

File-Level Changes

Change	Details	Files
Unified the TSV generation logic for both human-readable and machine-readable formats	Merged duplicate code paths into a single flow using a conditional flag isHumanFile Standardized header columns and their order across both formats Added conditional formatting using convertURIToLabel for human-readable files Preserved raw values for machine-readable files	src/components/ResultContainer.tsx
Updated test cases to reflect new column ordering	Adjusted column index assertions to match new column positions Updated expected values for session-related fields	cypress/e2e/ResultsTSV.cy.ts

Assessment against linked issues

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

Possibly linked issues

• Standardize query result files #389: The PR implements the standardization of query result files as described in the issue.
• [CI] Adding CodeQL Configuration, File Change Limitation Script, Linting, Formatting, and Type-Checking #45: The PR standardizes query result files, aligning with the issue's goal to update example generation.
• Standardize query result files #389: PR implements standardized formats for query result files, addressing the issue's requirements.

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[sourcery-ai]

Hey @rmanaem - I've reviewed your changes - here's some feedback:

Overall Comments:

• Please document the rationale for reordering the columns in the TSV output, as this represents a breaking change that could affect downstream tools.

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[surchs]

Thanks @rmanaem 🎉 !

Take a look at the space-separated arrays. My memory is that we wanted there to be no spaces (in both the human and machine files) between array elements (e.g. [T1Weighted,FlowWeighted] instead of [T1Weighted, FlowWeighted]

🧑‍🍳

[neurobagel-bot]

🚀 PR was released in v0.8.0 🚀