Check every index read, everywhere: noUncheckedIndexedAccess in tsconfig.json

[adamjohnwright]

Closes #345. The last 84 findings, in the two workspace libraries, are handled. noUncheckedIndexedAccess is now in tsconfig.json, so every build enforces it: both libraries, reactome-table-wc, the app and the embed. The flag comes out of the app and embed configs (they inherit it). The temporary counted check (scripts/check-indexed-access.mjs, its baseline, spec, npm script, and preflight and CI steps) is removed.

Over #413–#417: 346 findings (77 website, 95 + 85 pathway browser, 84 libraries, 5 templates), with no non-null assertions added (no-non-null-assertion stayed at 232).

reactome-table: the GSA form's spreadsheet

table.store.ts indexes a 2-D grid throughout and had two unit tests. So before rewriting it:

• table.store.session.spec.ts (new) drives the store through an editing session: generate, mapped import, typing (with the column maximum rising and falling), wrapping moves, range select, paste, delete, add and remove rows and columns by name and index, and an unmapped import. It snapshots the full state (cell values, selection marks, hidden cell, column maxima, start/stop, focus) after every step, plus every selector.
• The snapshots were recorded against the old store, and the rewrite reproduces them exactly.
• Proven sensitive: dropping a single trim() in paste fails two of its tests.

The rewrite keeps the store's behaviour on a missing row or cell. Reads that always threw on one still throw, through rowAt/cellAt/maxAt, which now name the coordinates. Reads across rows that are rectangular by construction (pushAll and addRow keep them so) go through atColumn, an explicit cast with that reason. Ranges.minMax uses Math.min/max in place of a two-element sort.

reactome-gsa-form

• An unknown parameter type from the GSA service (one added since) used to throw on typeToParse[type](…), taking the form down. It's now read as text: parserFor, with a new spec.
• An empty method list now gives no common parameters instead of a crash, and so do the covariances of a dataset with no annotations (?.slice). An empty annotation table still throws in initAnnotationColumns (now a RangeError saying the table has no rows), as it did before.
• comparisonGroup2Values already handled a missing list; its signature now says so.
• The rest are equivalent rewrites: split parts, transposed columns, and the pairing check, which still counts a missing value the way it always did.

Fixed after review

• Deleting the selected row broke the table (already on main). Select a cell in the last row, delete that row (the bin button), and Cells.select threw reading the stale selection. That ended the store's state stream and left the GSA form's table unusable. A cell that's gone now has nothing to un-mark. The session spec gains that step: it fails without the fix, and the earlier snapshots are unchanged (additions only).
• A missing GSA annotation value (a values list shorter than sample_ids) stays undefined (sent as null), as before. An earlier commit here had made it "".
• Review probe: the reviewer ran 20 store edge cases on main and on this branch: ragged and empty pastes and imports, reversed ranges, out-of-range selects, deleting the last row or column while selected. The final state matched in every case; only the error class differs (RangeError for TypeError), at the same point.

Templates found by the library builds

• table.component.html colSpan.
• The statistical-design group lookup.

Lint

With the flag in the root config, type-aware lint also sees spec and e2e files under it. Three index reads there (e2e/reacfoam.spec.ts, chat-handoff.spec.ts) now type-check as errors, which lint counts as any. They're guarded. Lint is unchanged at its baseline.

Tests

• Builds with the flag: build:libs, ng build reactome-table-wc, npm run build and build:embed all succeed.
• Full e2e suite locally: 388 passed, plus the 6 tests that skip themselves. After the last change, the analysis, analysis-results and reacfoam specs were rerun: 35 passed.
• Unit tests: 688 passed.
• Gates: check:lint, check:dead and format:check unchanged at their baselines.
• Render tests: ran live in the pre-push hook: ok.

🤖 Generated with Claude Code