feat(microbiology): add foundations and order routing (OGC-782)

[pmanko]

Summary

First implementation layer for the OGC-782 routine bacteriology workflow.

Scope

• Add microbiology workflow configuration to Test Catalog.
• Add organism, antibiotic, AST panel, breakpoint, and culture-setup foundations.
• Create the case and order-detail domain used by later workflow layers.
• Route configured culture analyses into microbiology cases.
• Provision test and demo scenarios through application services only, without SQL seeding, fixed primary keys, or DAO bypass.

Validation

• Focused service, controller, integration, fixture-architecture, and ORM coverage.
• Focused Test Catalog and microbiology component coverage.
• Java formatting and direct-database fixture guardrails.

Stack And Documents

• Specification PR: OGC-782 Microbiology MVP spec #3782
• Next layer: feat(microbiology): add case workbench and manual AST (OGC-782) #4134
• Feature specification
• Engineering plan
• Execution roadmap

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 4e33d1aaaa

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[pmanko]

MVP evidence vs mock comparison added:

specs/782-ogc-782-microbiology-mvp-spec/evidence/mock-comparison-2026-06-27.md

Key takeaway: the Playwright screenshots/video prove the behavioral MVP path through final release, but they are not mock-fidelity proof. The current UI is a functional vertical workbench, while the OpenELIS-work mocks describe a guided workflow shell with richer case progress, AST table, expert-review, critical-notification, and WHONET mapping/export surfaces.

I also flagged two concrete evidence/UX issues:

• Some tall full-page screenshots show the sticky OpenELIS header mid-page, making the evidence hard to read.
• After FINAL_RELEASED, the final release button remains visible/enabled-looking and should get a post-release state review.

[pmanko]

Design-parity pass pushed in 23b577550.

What changed:

• Reworked the microbiology case view into a mock-aligned workbench: progress rail, next-step callout, case-info strip, highlighted inoculation/setup card, separate timeline, isolate card, AST table, critical-communication card, and report/WHONET readiness cards.
• Fixed post-final-release UX so the final release action is no longer offered after FINAL_RELEASED.
• Refreshed the MVP evidence notes after comparing against the openelis-work case-workbench mock.

Validation run locally:

• cd frontend && npm test -- MicrobiologyCaseView.test.jsx IsolatePanel.test.jsx AstEntryPanel.test.jsx CriticalCommunicationPanel.test.jsx ReportReadinessPanel.test.jsx
• cd frontend && npm run pw:test -- playwright/tests/demo/core/ogc-782-microbiology-mvp.spec.ts --project=core-demo
• cd frontend && npm run pw:test -- playwright/tests/demo/core/ogc-782-microbiology-mvp.spec.ts --project=core-demo-video

Updated local evidence:

• Video: /Users/pmanko/.codex/worktrees/1c9d/OpenELIS-Global-2/frontend/test-results/demo-core-ogc-782-microbio-3f6cc-ual-AST-override-and-review-core-demo-video/video.webm
• Bundle zip: /Users/pmanko/.codex/worktrees/1c9d/OpenELIS-Global-2/specs/782-ogc-782-microbiology-mvp-spec/evidence/mvp-checkpoint-2026-06-27.zip
• Design-parity comparison: /tmp/ogc-782-mock-compare/design-parity-case-workbench-2026-06-27.png

Known remaining mock gaps are feature-depth gaps, not raw layout gaps: richer isolate ID, multi-row AST metadata, expert review queue, and WHONET mapping/export UI are still future slices.

[pmanko]

Updated MVP visual/evidence polish in 16729a1c1.

What changed:

• Slowed the guided Playwright walkthrough and added clearer step cards/context.
• Switched evidence capture to focused viewport/card screenshots and added sticky-header scroll margin so captured cards are not clipped.
• Replaced raw microbiology enums in the workbench with user-facing labels (Received, Bacteriology, Setup Recorded, In Progress, Reviewed, Final Released, etc.).
• Locked AST controls after review so the reviewed state no longer implies post-review edits are open.
• Refreshed the evidence notes under specs/782-ogc-782-microbiology-mvp-spec/evidence/.

Validated:

• cd frontend && npm test -- MicrobiologyCaseView.test.jsx IsolatePanel.test.jsx AstEntryPanel.test.jsx CriticalCommunicationPanel.test.jsx ReportReadinessPanel.test.jsx -> 5 files / 7 tests passed.
• cd frontend && npm run pw:test -- playwright/tests/demo/core/ogc-782-microbiology-mvp.spec.ts --project=core-demo-video -> 2 passed.
• Key screenshots manually inspected for design parity/readability: overview, reviewed AST, final readiness.

Fresh local evidence:

• Video: /Users/pmanko/.codex/worktrees/1c9d/OpenELIS-Global-2/frontend/test-results/demo-core-ogc-782-microbio-3f6cc-ual-AST-override-and-review-core-demo-video/video.webm
• MP4 bundle: /Users/pmanko/.codex/worktrees/1c9d/OpenELIS-Global-2/specs/782-ogc-782-microbiology-mvp-spec/evidence/mvp-checkpoint-2026-06-27/videos/demo-core-ogc-782-microbio-3f6cc-ual-AST-override-and-review-core-demo-video.mp4
• Bundle zip: /Users/pmanko/.codex/worktrees/1c9d/OpenELIS-Global-2/specs/782-ogc-782-microbiology-mvp-spec/evidence/mvp-checkpoint-2026-06-27.zip
• Screenshots: /Users/pmanko/.codex/worktrees/1c9d/OpenELIS-Global-2/frontend/e2e-evidence/ogc-782-01-case-workbench-overview.png through ogc-782-08-final-released-readiness.png.

Known console noise remains the existing unrelated React Intl missing-message output for analyzer/nav labels during auth; the microbiology walkthrough itself passed.

[pmanko]

Addressed the three Codex review findings and the frontend Playwright CI failure in 07cd10b0e.

Fixes:

• Final release now blocks when a case has an open critical communication with follow-up required. The readiness API also reports CRITICAL_FOLLOW_UP_REQUIRED, so the UI/readiness state does not claim ready and then fail only after click.
• Final release now routes through MicroCaseStateService.advanceStage(... FINAL_RELEASED ...), so invalid transitions such as RECEIVED -> FINAL_RELEASED are rejected by the existing transition guard before release fields are set.
• WHONET readiness now checks referenced MicroOrganism.whonetCode and MicroAntibiotic.whonetCode, not just local IDs. Missing export mappings produce ORGANISM_MAPPING_REQUIRED / ANTIBIOTIC_MAPPING_REQUIRED blockers.
• Playwright CI failure root cause: pw-bucket-guard.mjs reads named bucket constants from playwright.config.ts, but core foundational specs were only listed inline in the core-app project. Added CORE_FOUNDATIONAL_TESTS and pointed core-app at it, so the guard can classify foundational/core/**/*.spec.ts.

Local validation:

• mvn spotless:apply
• mvn -Dtest=MicroCaseReadinessServiceTest,MicroReportReleaseServiceTest,MicroWhonetReadinessServiceTest test -> 12 tests passed.
• cd frontend && npx prettier --write playwright.config.ts
• cd frontend && npm run lint -> Playwright ESLint passed.
• cd frontend && npm run pw:guard -> bucket guard passed.

[pmanko]

Live AMR deployment and UAT checkpoint

• Target: https://amr.openelis-global.org
• Deployment: 20260725T003108Z-c44c3ad0ce35
• Deployed app SHA: c44c3ad0ce35d1502d9ed217f3e26aa88e309dc1
• Review-tooling SHA: 2cf9dd4e5794e2ce46a568c295d8093ae51bf33e
• Scope: app; schema-affecting: false; health + route smoke: passed
• Live Playwright: auth + feature 2 passed (6.6s); final evidence run 1 passed (4.0s)
• Grist checklist: 10 stable steps, revision 364c75677839c0aed225ecfa75e5c0912c07840a1925a14c9dd30bf2ed2d7d95

Evidence: README · MP4 · overlay screenshot

Two follow-up signals are recorded, not hidden: all live Grist rows currently have required=false, and nested routes emit route-relative service-worker 404/MIME console noise. Neither blocked the tested workflow.

[pmanko]

Follow-up pushed in 5a00513a4 after the live AMR UAT signal.

• Fixed the production service-worker registration URL. The former relative ./service-worker.js resolved under nested microbiology case URLs; both normal registration and notification subscription now use the Vite application base.
• Added serviceWorkerRegistration.test.js covering root and context-path asset URLs.
• Integrated the already-green TypeScript toolchain commit from #3929 as 489b7ecae, so ongoing OGC-782 work uses the current compatible compiler/tooling while that focused PR completes review.

Validation:

• npx vitest run src/serviceWorkerRegistration.test.js — 2 passed
• targeted ESLint for the helper/test and Prettier for all touched files — passed
• npm run build — passed

Note: linting the existing SlideOverNotifications.jsx independently still reports its pre-existing hook-order rule and unused-variable warnings; this change neither introduces nor suppresses them. Existing OGC-782 Playwright coverage continues to cover configured navigation and canonical deep-link URLs.

[pmanko]

Live AMR redeployment and fixture-integrity checkpoint (0b88c8a08 docs the deployment; app runtime is 9d0c55b6f):

• Full schema-affecting app deployment: 20260728T222317Z-9d0c55b6fd3c
• Backend-only recreation for the AMR demo UAT endpoint: 20260729T035240Z-9d0c55b6fd3c
• Review tooling deployed at 427aa5feb; Grist now renders 4 stories / 10 required steps, revision e4b7ae19652e786a09aeead8fd39567bb66dc487fef9f9a8b0ac75f7aa0f0a37
• The old direct-SQL fixture path has been removed. Provisioning now authenticates to OpenELIS and calls the property-gated service. Two runs with key review-amr-microbiology-mvp returned the same accession UATMICRO01C82736AB and case IDs.
• Exact case: https://amr.openelis-global.org/Microbiology/cases/a65d620c-c96b-4627-9d69-9c00ba310551?workflow=BACTERIOLOGY&sort=newest&section=isolates
• Evidence: live-deployment-2026-07-28.md

This supersedes the July 24 comment's optional-step and route-relative service-worker observations. Current review findings remain explicit in the evidence: received-case progress labels need semantic review, 15 legacy SQL-seeded demo rows remain, and the unrelated global notification subscription surface still logs fetch/JSON errors.

[pmanko]

CI remediation pushed in 6f941e6 and 46ab388.\n\nRoot cause: legacy DBUnit tests truncate shared reference tables, leaving stale global status cache entries and no active Method for later microbiology integration tests.\n\nFix:\n- microbiology fixtures now provision their minimum status and Method prerequisites through the service layer\n- identifiers and status codes are generated; no SQL, DAO bypass, fixed primary keys, or migration\n- StatusOfSample duplicate detection now compares its numeric code as a numeric value instead of applying lower() to it\n- regression coverage includes stale-cache rollback and the exact ResultsValidationUtilityTest -> MicroCaseIntegrationTest order\n\nLocal verification:\n- mvn spotless:check\n- mvn clean install -Dspotless.check.skip=true\n- 4,660 tests, 0 failures, 0 errors, 14 skipped\n- WAR packaging completed successfully in 6m32s\n\nExternal AMR UAT remains independently blocked and is not represented as complete by this CI remediation.

[github-actions]

👋 Hi, @pmanko,
Conflicts have been detected against the base branch. Please rebase your branch against the base branch.

---

This message is automatically generated by prince-chrismc/label-merge-conflicts-action so don't hesitate to report issues/improvements there.

[Copilot]

Copilot wasn't able to review this pull request because it exceeds the maximum number of lines (20,000). Try reducing the number of changed lines and requesting a review from Copilot again.

[github-actions]

👋 Hi, @pmanko,
Conflicts have been detected against the base branch. Please rebase your branch against the base branch.

---

This message is automatically generated by prince-chrismc/label-merge-conflicts-action so don't hesitate to report issues/improvements there.