Add qPCR + TapeStation support, table-pending transitions, and run files/report refinements

[wasimxyz]

Summary

This branch adds first-class support for two new instrument types (qPCR and TapeStation), introduces a shared "stale table" pending treatment that ties every server-side query-string change to a React transition, and delivers a batch of run-detail / run-files / report-section refinements.

Changes

qPCR + TapeStation instrument support

• New Drizzle migration web-app/drizzle/0006_qpcr_tape_station.sql extending instrument_type with qpcr and tape_station, with matching enum + VALID_INSTRUMENT_TYPES entries in web-app/lib/db/schema.ts.
• New run-detail variants web-app/components/runs/variants/qpcr-run-detail.tsx and tape-station-run-detail.tsx, wired into the variant dispatcher in web-app/components/runs/variants/index.tsx.
• New qPCR runs table web-app/components/instruments/runs-table/qpcr-runs-table.tsx with a filterable "Dye Channels" column backed by getQpcrFilterOptions and dye_channel search param (web-app/lib/api/instrument-runs.ts, web-app/lib/search-params.ts, filterable-column-header.tsx).
• New qPCR / TapeStation metadata badges and hasQpcrMetadata / hasTapeStationMetadata helpers in web-app/components/runs/run-metadata-badges.tsx; dye-channel color helper in web-app/lib/instrument-colors.ts.
• Human-readable labels for qpcr / tape_station in web-app/components/instruments/edit-instrument-dialog.tsx.

Table pending / stale treatment

• New web-app/components/table-pending.tsx exporting TablePendingProvider, TablePendingBoundary, and useTablePending. Provides a React transition that sibling useQueryState(s) calls hook into via startTransition, with a 120 ms delay before any visible change to avoid flicker on fast fetches.
• Applied to the dashboard (app/page.tsx + dashboard/runs-toolbar.tsx), per-instrument runs (app/instruments/[instrumentId]/page.tsx + instrument-runs-toolbar.tsx + filterable-column-header.tsx), and the watcher event log (watcher-detail-tabs.tsx + event-log-toolbar.tsx + event-log.tsx).
• pagination-nav.tsx now reads the pending state, dims to 60% opacity, blocks pointer events, and sets aria-busy while the RSC payload streams in; Prev / Next disable themselves instantly to prevent queued double-clicks.
• New @keyframes table-pending-slide in web-app/app/globals.css drives the thin sliding indeterminate bar.

Run files table

• Extracted the presentational table into a new web-app/components/runs/run-files-table.tsx (status badge logic, selection column, row actions). run-files-section.tsx now owns only state + handlers.
• Added a "Type" column (raw / processed) and a stable secondary sort that always lists raw files before processed files within each sort field.
• Allow completed files to be reprocessed (previously only failed); reprocess action now gates on REPROCESSABLE_STATUSES = { completed, failed }.

Run report section

• run-report-section.tsx now renders PDFs (by content type or .pdf extension) in an inline <iframe> alongside processed images, so qPCR / TapeStation exports render in-page. Count label updated to N file(s).
• Removed unused web-app/components/runs/report-data-table.tsx.

File size fix for processed artifacts

• lambda/src/data_hub_lambda/azure_600_gel_doc/process_file.py and spectramax_plate_reader/process_file.py now pass size_bytes=...stat().st_size when recording processed outputs, so the Total Size column accounts for derived PNG / CSV files.

Misc UX

• Empty RunMetadata now returns null instead of the "No metadata recorded yet" placeholder, cleaning up run-detail pages when there is nothing to show.

Breaking changes

• New Postgres migration 0006_qpcr_tape_station must be applied before deploy; it adds two values to the instrument_type enum. No existing data is altered.
• No API / route contract changes.

Driveby changes

• Ran the formatter across touched files (chore: Run formatter, 4fed033).
• Tightened pagination-nav.tsx (atPrev / atNext locals, collapsed duplicated className ternaries).
• InstrumentRunsTable / dispatcher updated to accept qpcrFilterOptions alongside the existing plate-reader / gel-doc options.
• Edit-instrument dialog label map gained entries for qpcr and tape_station.

Testing

• Apply migration 0006_qpcr_tape_station.sql in a clean staging DB; confirm the instrument_type enum now includes qpcr and tape_station.
• Create a qPCR instrument via the edit dialog; verify the label renders as "qPCR".
• Upload a qPCR run and confirm it appears in the new QpcrRunsTable with a populated "Dye Channels" column; verify the column dropdown filter round-trips via ?dye_channel=....
• Open a qPCR run detail page; verify qPCR metadata badges render and metadata section is hidden when metadata is empty.
• Upload a TapeStation run with a PDF report; verify the Report Data section renders the PDF in the inline viewer and "Open in new tab" works.
• On the dashboard and instrument runs tables, apply a toolbar filter and click pagination; verify the table dims to ~60% opacity, the sliding bar appears only after fast fetches complete without flicker, and pagination is non-interactive during the transition.
• On the watcher Event Log tab, change filters / paginate and verify the same pending treatment applies.
• Reprocess a completed file from the files table; verify the action is offered (was previously hidden) and existing report data is cleared.
• In the run files table, confirm the new "Type" column shows "raw" / "processed" and raw files sort before processed files regardless of the active sort field.
• Re-run a gel doc / plate reader processing job and verify the Total Size column on the run row includes the processed artifact bytes.

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Project	Deployment	Actions	Updated (UTC)
data-hub	Ready	Preview, Comment	Apr 21, 2026 7:27pm