IGVF-3459 Add file download to pseudobulk-set pages

[forresttanaka]

Code Review — IGVF-3459-pseudobulk-dpwnload

Reviewed by GitHub Copilot (Claude Sonnet 4.6)

---

Summary of Changes

This branch converts pages/pseudobulk-sets/[id].js from JavaScript to TypeScript and adds a full pseudobulk set detail page. It also introduces several type-safety and refactoring improvements across the lib layer that benefit multiple pages.

---

Files Reviewed

File	Change
pages/pseudobulk-sets/[id].tsx	New — JS→TS conversion, full detail page
lib/file-sets.ts	New — extracted file-set request helpers
lib/next-js.ts	New — shared PageProps interface
lib/database-object.ts	Enhanced type guards, pathsFromDatabaseObjects
lib/common-requests.ts	Stronger return types, generic requestSupersedes<T>
lib/files.ts	getFilesFileSets, requestFilesQualityMetrics, removed ad-hoc type guards
lib/errors.ts	Generic errorObjectToProps<T>
lib/search-results.ts	New isSearchResults type guard
lib/facets.ts	Use isSearchResults instead of cast
lib/types.ts	isEmbeddedArray fix, LinkTo<T> type
globals.d.ts	LinkTo<T> on union fields, SearchResults decoupled from DatabaseObject, status required, submitter_comment moved to DatabaseObject
lib/data-grid.ts	CellContentProps fields made required
lib/ontology-terms.ts	profiles accepts null
components/add.tsx	void on unhandled promises
components/file-graph/file-set-modal.tsx	Typed grid config, corrected input_file_for guard
components/institutional-certificate-table.tsx	Typed grid config, removed redundant casts
components/search/list-renderer/index.tsx	Typed reduce accumulators
pages/assays.tsx	isMatrixResultsObject guard, cleaner variable naming
pages/computational-tools.tsx	Use isSearchResults, remove cast
pages/users/[uuid].tsx	Minor type cleanup
lib/__tests__/…	Tests added/updated throughout

---

Observations

• lib/file-sets.ts is a clean extraction that eliminates copy-pasted patterns across page files.
• pathsFromDatabaseObjects handles both the embedded-object and path-string cases uniformly, which simplifies all call sites.
• errorObjectToProps<T> being generic removes as unknown as casts that were scattered across getServerSideProps implementations.
• isDatabaseObjectArray returning false for empty arrays is consistent with isDatabaseObjectArrayOfType and isEmbeddedArray, but callers should be aware this is a deliberate convention.
• isSearchResults checking @type.length === 1 is stricter than other type guards in the codebase (which use .includes()). This is fine as long as the backend never adds extra entries to @type on search responses.
• Making status required on DatabaseObject is correct for well-formed objects but may require attention in test fixtures that omit it — the updated tests handle this.

---

Conclusion

The branch is in good shape. The overall direction — replacing ad-hoc casts and inline type guards with shared, well-tested utilities — makes the codebase meaningfully safer and easier to maintain. Ready to merge.

[forresttanaka]

Code Review: IGVF-3459 Add file download to pseudobulk-set pages

• Model: GPT-5.3-Codex
• Branch: IGVF-3459-pseudobulk-dpwnload
• Compared against: dev...HEAD
• Date: 2026-05-07

Findings

Low

1. Global type-guard semantics changed for empty arrays in lib/types.ts.

• isEmbeddedArray now returns false for empty arrays (value.length > 0 required).
• This can alter behavior at call sites that previously treated an empty embedded array as valid embedded data.
• Existing tests cover non-empty and invalid cases, but there is no explicit regression test documenting intended behavior for the empty-array case after this change.

Not a Finding (Intent Clarified)

• Input file sets on pseudobulk pages are still rendered.
• Simplified related-set data for pseudobulk input file sets (control/auxiliary/measurement meta arrays) is intentional because those linked types cannot appear for pseudobulk sets.

Testing Notes

• This review is static (diff-based).
• I did not execute the full test suite in this review pass.

Conclusion

• The branch successfully implements pseudobulk file-download related changes and improves type safety across several modules.
• No blocking issues remain from input file-set simplification because that behavior is intentionally constrained for pseudobulk sets.
• Remaining review risk is limited to the global empty-array semantics change in isEmbeddedArray.

[Copilot]

Pull request overview

This PR adds/updates pseudobulk-set detail functionality (including file download actions) while converting the pseudobulk-set page to TypeScript and introducing shared request/type-guard utilities across the lib layer to reduce casting and improve safety.

Changes:

• Replaces the pseudobulk set detail page (pages/pseudobulk-sets/[id]) with a TypeScript implementation and server-side data fetching for associated objects (files, samples, donors, publications, etc.).
• Adds shared helpers for file-set–related requests and strengthens several shared request utilities/type guards.
• Updates global typings and expands Jest coverage for the new helpers/guards.

Reviewed changes

Copilot reviewed 26 out of 27 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
pages/pseudobulk-sets/[id].tsx	New TS pseudobulk-set detail page with server-side data loading and download UI integration
pages/pseudobulk-sets/[id].js	Removes the prior JS implementation of the pseudobulk-set page
pages/users/[uuid].tsx	Tightens SSR typing and adds a params not-found guard
pages/computational-tools.tsx	Uses isSearchResults guard and updates SSR error handling path
pages/assays.tsx	Adds a matrix-response guard and tweaks table header sizing
components/add.tsx	Adds void for unhandled promises; adjusts types
components/file-graph/file-set-modal.tsx	Strengthens guards for mixed embedded/link fields; improves grid typing
components/institutional-certificate-table.tsx	Types the sortable grid configuration and simplifies render signatures
components/search/list-renderer/index.tsx	Adds explicit accumulator typings to reduce calls
lib/file-sets.ts	New helper module for requesting associated file-set linked objects
lib/files.ts	Adds helpers for file-set retrieval and for requesting reference/quality-metric objects
lib/common-requests.ts	Strengthens return types and generics for requests (files, quality metrics, supersedes, etc.)
lib/database-object.ts	Enhances DB object guards and adds pathsFromDatabaseObjects
lib/errors.ts	Makes errorObjectToProps generic for SSR typing
lib/facets.ts	Uses isSearchResults instead of casting for facet retrieval
lib/search-results.ts	Adds isSearchResults type guard
lib/types.ts	Adjusts isEmbeddedArray behavior to require non-empty arrays
lib/ontology-terms.ts	Allows profiles to be null in preferred assay title mapping
lib/next-js.ts	New shared PageProps shape for SSR-returned page props
lib/data-grid.ts	Makes CellContentProps.id and .source required in typings
globals.d.ts	Refactors LinkTo<T> usage, strengthens DatabaseObject, and adjusts SearchResults definition
lib/tests/search-results.test.ts	Adds tests for isSearchResults
lib/tests/files.test.ts	Adds tests for new file helpers and updates fixtures
lib/tests/file-sets.test.ts	New tests for lib/file-sets request helpers
lib/tests/facets.test.ts	Updates facet tests to satisfy the new isSearchResults guard
lib/tests/database-objects.test.ts	New tests for database-object guards and pathsFromDatabaseObjects
lib/tests/common-requests.test.ts	Updates fixtures/expectations for typed request changes

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.