feat(microbiology): add case workbench and manual AST (OGC-782) by pmanko · Pull Request #4134 · DIGI-UW/OpenELIS-Global-2

pmanko · 2026-08-25T22:15:56Z

Summary

Second OGC-782 implementation layer: the routine bacteriology case workbench and manual antimicrobial susceptibility testing workflow.

Scope

Add the case workbench, activity timeline, and focused workflow sections.
Create isolates and update organism identification.
Create AST runs with multiple readings.
Apply configured breakpoints, support reviewed overrides, and derive audit actors from the authenticated request.
Reuse shared microbiology service and Carbon interaction patterns.

Validation

Focused case, isolate, AST, controller, and ORM coverage.
Focused workbench and AST component coverage.
Registered foundational Playwright case-workbench journey under core-app.

Stack And Documents

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+    @PostMapping("/runs")
+    @PreAuthorize("isAuthenticated()")
+    public ResponseEntity<MicroAstRunForm> startRun(@RequestBody MicroAstRunRequestForm request,


Require a result-entry role for AST mutations

Replace isAuthenticated() with the appropriate result-entry/supervisor role check for AST writes. As implemented, any authenticated account—including users without RESULTS privileges—can start runs, enter readings, override interpretations, and mark runs reviewed; the new frontend route is likewise configured without a role. Comparable result-entry controllers require hasRole('RESULTS'), and these clinical mutations must be protected by RBAC.

AGENTS.md reference: AGENTS.md:L473-L485

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+        MicroAstRun run = runDAO.get(runId).orElseThrow(() -> new IllegalArgumentException("AST run not found"));
+        MicroIsolate isolate = isolateDAO.get(run.getIsolateId())
+                .orElseThrow(() -> new IllegalArgumentException("Isolate not found"));
+        requireMutableCase(isolate.getCaseId());
+        run.setStatus(MicroAstRunStatus.REVIEWED.name());


Reject reviewing AST runs with no readings

Validate that the run has at least one reading before changing it to REVIEWED. The React button enforces this only client-side, so an authenticated caller can POST directly to /review, review an empty run, and make MicroCaseReadinessServiceImpl report a clinically significant isolate as final-release ready without any AST result. This invariant belongs in the service before persistence.

AGENTS.md reference: AGENTS.md:L340-L349

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+        MicroAstRun run = runDAO.get(runId).orElseThrow(() -> new IllegalArgumentException("AST run not found"));
+        MicroIsolate isolate = isolateDAO.get(run.getIsolateId())
+                .orElseThrow(() -> new IllegalArgumentException("Isolate not found"));
+        requireMutableCase(isolate.getCaseId());


Prevent mutations after an AST run is reviewed

Reject recordReading and overrideReading when the parent run is already REVIEWED. Only the UI disables these actions; direct REST calls can still add a new antibiotic or alter an override after review, while readiness remains true and no second review is required, allowing unreviewed clinical changes to flow toward reporting. The run-state validation should be enforced in the service before writing.

AGENTS.md reference: AGENTS.md:L340-L349

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+        List<MicroAstRun> runs = astRunDAO.getByIsolateId(isolateId);
+        for (MicroAstRun run : runs) {
+            if (MicroAstRunStatus.REVIEWED.name().equals(run.getStatus())) {
+                return true;


Make an unreviewed repeat run block readiness

Do not return readiness merely because any historical run is reviewed. When an isolate has a reviewed run and a newer repeat/retest run is still IN_PROGRESS, this loop returns true for the old run, so the case is presented as final-release ready even though the current AST work has not been reviewed; readiness must account for the latest or otherwise active run.

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+        reading.setOverrideInterpretation(overrideInterpretation.name());
+        reading.setOverrideReason(overrideReason);
+        MicroAstReading updated = readingDAO.update(reading);
+        recordActivity(isolate.getCaseId(), MicroCaseActivityType.AST_READING_OVERRIDDEN, performedBy,
+                "AST interpretation overridden", "{\"readingId\":\"" + readingId + "\"}");


Preserve every AST override in the audit history

Persist an append-only override record, or include the prior/new interpretation and reason in an immutable audit record. A second override currently overwrites the only overrideInterpretation and overrideReason values, while the activity stores only readingId, so the first interpretation change and its reason can no longer be reconstructed for the required clinical audit trail.

AGENTS.md reference: AGENTS.md:L479-L485

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+                  disabled={
+                    busy ||
+                    !!currentRun ||
+                    !selectedIsolateId ||
+                    !selectedPanelId


Allow a new AST run after review

Enable starting another run once the current run is no longer in progress. currentRun falls back to the last historical run whenever runs is nonempty, and !!currentRun therefore disables the start button forever after the first run is reviewed, making the specified repeat/retest workflow inaccessible from the workbench.

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chatgpt-codex-connector · 2026-08-25T22:20:44Z

+    private static final String DEFAULT_BREAKPOINT_AUTHORITY = "CLSI";
+    private static final String DEFAULT_BREAKPOINT_VERSION = "2026";


Resolve the default breakpoint standard from configuration

Remove the hard-coded CLSI/2026 fallback and resolve the deployment-configured default, or require an explicit snapshotted standard. For runs created without breakpointStandardId, installations using EUCAST, another CLSI edition, or a future yearly standard get no rule and silently classify every reading as NO_BREAKPOINT despite having active breakpoint data.

AGENTS.md reference: AGENTS.md:L262-L275

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Pull request overview

Adds the second implementation layer for OGC-782 by introducing the microbiology case workbench UI and the manual AST workflow end-to-end (schema → services → REST → React UI → tests), building on the microbiology foundations delivered in #3789.

Changes:

Introduce manual AST domain (run + readings), persistence (Liquibase + JPA), service logic (interpretation/override/review), and REST endpoints.
Add case workbench UI (timeline, isolates, AST entry) plus supporting API client functions and route wiring.
Add/extend unit, integration, ORM, controller, and Playwright tests to cover the new workflows.

Reviewed changes

Copilot reviewed 67 out of 67 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
src/test/resources/persistence/test-persistence.xml	Registers new microbiology AST entities for test persistence.
src/test/java/org/openelisglobal/microbiology/service/MicroIsolateServiceTest.java	Expands isolate tests (organismId normalization, final-release guard).
src/test/java/org/openelisglobal/microbiology/service/MicroCaseReadinessServiceTest.java	Adds readiness tests for final-release gating based on AST review.
src/test/java/org/openelisglobal/microbiology/service/MicroBreakpointServiceTest.java	Adds test for listing active breakpoint standards.
src/test/java/org/openelisglobal/microbiology/service/MicroAstServiceTest.java	Adds unit tests for AST run creation and interpretation behavior.
src/test/java/org/openelisglobal/microbiology/service/MicroAstInterpretationServiceTest.java	Adds interpretation + override validation tests.
src/test/java/org/openelisglobal/microbiology/MicrobiologyOrmValidationTest.java	Extends ORM validation coverage to AST entities.
src/test/java/org/openelisglobal/microbiology/MicrobiologyArchitectureTest.java	Extends architecture test to cover all new microbiology controllers.
src/test/java/org/openelisglobal/microbiology/MicroAstIntegrationTest.java	Adds integration tests covering AST run/read/override/review flows.
src/test/java/org/openelisglobal/microbiology/controller/MicroCaseRestControllerTest.java	Expands controller tests for new activity/order/isolate endpoints + actor behavior.
src/test/java/org/openelisglobal/microbiology/controller/MicroCaseLookupRestControllerTest.java	Updates constructor wiring for controller tests.
src/test/java/org/openelisglobal/microbiology/controller/MicrobiologyRestExceptionHandlerTest.java	Adds tests for locked-case REST error mapping.
src/test/java/org/openelisglobal/AppTestConfig.java	Updates component scan formatting/structure for tests.
src/main/resources/persistence/persistence.xml	Registers new AST entities in main persistence unit.
src/main/resources/liquibase/3.5.x.x/base.xml	Includes new microbiology AST-related changesets.
src/main/resources/liquibase/3.5.x.x/056-microbiology-ast-breakpoint-standard.xml	Adds nullable breakpoint standard FK on AST run.
src/main/resources/liquibase/3.5.x.x/053-microbiology-manual-ast.xml	Creates AST run/reading tables + constraints and rollback.
src/main/java/org/openelisglobal/microbiology/valueholder/MicroCaseActivityType.java	Adds activity types for AST events.
src/main/java/org/openelisglobal/microbiology/valueholder/MicroAstRunStatus.java	Introduces AST run status enum.
src/main/java/org/openelisglobal/microbiology/valueholder/MicroAstRun.java	Adds JPA entity for AST runs.
src/main/java/org/openelisglobal/microbiology/valueholder/MicroAstReading.java	Adds JPA entity for AST readings + overrides.
src/main/java/org/openelisglobal/microbiology/valueholder/MicroAstMethod.java	Adds MIC/ZONE method enum.
src/main/java/org/openelisglobal/microbiology/valueholder/MicroAstInterpretation.java	Adds interpretation enum including NO_BREAKPOINT.
src/main/java/org/openelisglobal/microbiology/service/MicroIsolateServiceImpl.java	Adds mutation guard + organismId normalization.
src/main/java/org/openelisglobal/microbiology/service/MicroCaseReadinessServiceImpl.java	Implements readiness calculation based on isolate AST review status.
src/main/java/org/openelisglobal/microbiology/service/MicroCaseReadinessService.java	Adds readiness service contract.
src/main/java/org/openelisglobal/microbiology/service/MicroCaseMutationGuard.java	Centralizes final-release immutability rule for microbiology cases.
src/main/java/org/openelisglobal/microbiology/service/MicroCaseLockedException.java	Adds domain exception surfaced as 409 for locked cases.
src/main/java/org/openelisglobal/microbiology/service/MicroAstServiceImpl.java	Implements AST run/read/override/review behavior + activity recording.
src/main/java/org/openelisglobal/microbiology/service/MicroAstService.java	Adds AST service contract.
src/main/java/org/openelisglobal/microbiology/service/MicroAstInterpretationServiceImpl.java	Implements MIC/ZONE breakpoint interpretation + override validation.
src/main/java/org/openelisglobal/microbiology/service/MicroAstInterpretationService.java	Adds interpretation service contract.
src/main/java/org/openelisglobal/microbiology/form/MicroIsolateRequestForm.java	Adds isolate request DTO for REST endpoints.
src/main/java/org/openelisglobal/microbiology/form/MicroCaseReadinessForm.java	Adds readiness DTO (blockers + ready flag).
src/main/java/org/openelisglobal/microbiology/form/MicroCaseActivityRequestForm.java	Adds case activity mutation request DTO.
src/main/java/org/openelisglobal/microbiology/form/MicroAstRunRequestForm.java	Adds AST run request DTO.
src/main/java/org/openelisglobal/microbiology/form/MicroAstRunForm.java	Adds AST run response DTO including readings.
src/main/java/org/openelisglobal/microbiology/form/MicroAstReadingRequestForm.java	Adds AST reading request DTO.
src/main/java/org/openelisglobal/microbiology/form/MicroAstReadingForm.java	Adds AST reading response DTO.
src/main/java/org/openelisglobal/microbiology/form/MicroAstOverrideRequestForm.java	Adds AST override request DTO.
src/main/java/org/openelisglobal/microbiology/daoimpl/MicroAstRunDAOImpl.java	Adds DAO query for runs by isolate.
src/main/java/org/openelisglobal/microbiology/daoimpl/MicroAstReadingDAOImpl.java	Adds DAO query for readings by run.
src/main/java/org/openelisglobal/microbiology/dao/MicroAstRunDAO.java	Adds AST run DAO contract.
src/main/java/org/openelisglobal/microbiology/dao/MicroAstReadingDAO.java	Adds AST reading DAO contract.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicroIsolateRestController.java	Adds isolate create/update endpoints with authenticated actor.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicroCaseRestController.java	Adds case activity and order-detail endpoints; uses authenticated actor helper.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicroCaseReadinessRestController.java	Adds readiness endpoint for microbiology cases.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicrobiologyRestExceptionHandler.java	Maps locked-case domain exception to 409 with structured error body.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicrobiologyRestControllerSupport.java	Adds shared authenticated actor lookup + 401 enforcement.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicroAstRestController.java	Adds AST endpoints (runs, readings, override, review).
specs/782-ogc-782-microbiology-mvp-spec/tasks.md	Marks M4/M5 tasks complete in the spec workflow.
specs/782-ogc-782-microbiology-mvp-spec/playwright-plan.md	Adds Playwright flow plan and evidence references.
frontend/src/pages/MicrobiologyPage.jsx	Adds microbiology page wrapper around case workbench.
frontend/src/languages/en.json	Adds microbiology UI message IDs for workbench + AST.
frontend/src/components/microbiology/MicrobiologyService.js	Adds frontend API functions for cases, isolates, readiness, and AST.
frontend/src/components/microbiology/MicrobiologyCaseView.jsx	Adds case workbench shell: header + timeline + isolates + AST panels.
frontend/src/components/microbiology/IsolatePanel.jsx	Adds isolate create/edit UI and organism selection integration.
frontend/src/components/microbiology/CaseTimelinePanel.jsx	Adds activity timeline display + stage advancement UI.
frontend/src/components/microbiology/AstEntryPanel.jsx	Adds AST run setup, reading entry, override, review, and readiness display.
frontend/src/components/microbiology/tests/MicrobiologyCaseView.test.jsx	Adds component tests for workbench loading and activity/isolate refresh behaviors.
frontend/src/components/microbiology/tests/IsolatePanel.test.jsx	Adds tests for isolate creation/edit flow and read-only state.
frontend/src/components/microbiology/tests/AstEntryPanel.test.jsx	Adds tests covering AST start/read/override/review UI behavior.
frontend/src/App.jsx	Adds route for microbiology case workbench page.
frontend/playwright/tests/foundational/core/microbiology-case-workbench.spec.ts	Adds foundational Playwright coverage for setup + isolate creation.
frontend/playwright/tests/demo/core/ogc-782-microbiology-mvp.spec.ts	Adds demo Playwright journey for end-to-end microbiology MVP flow.
frontend/playwright/helpers/seed-microbiology-data.ts	Adds helper to seed/cleanup microbiology data for Playwright scenarios.
frontend/playwright.config.ts	Registers new microbiology tests in the Playwright project allowlists.

Suppressed comments (1)

src/main/java/org/openelisglobal/microbiology/controller/rest/MicroAstRestController.java:71

MicroAstInterpretation.valueOf(request.overrideInterpretation) will throw (NPE/IllegalArgumentException) for missing/invalid input and currently results in a 500. This should be treated as a client error (400) with a clear message.

    public ResponseEntity<MicroAstReadingForm> overrideReading(@PathVariable String readingId,
            @RequestBody MicroAstOverrideRequestForm request, HttpServletRequest httpRequest) {
        MicroAstReading reading = astService.overrideReading(readingId,
                MicroAstInterpretation.valueOf(request.overrideInterpretation), request.overrideReason,
                authenticatedUserId(httpRequest));
        return ResponseEntity.ok(toReadingForm(reading));

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github-project-automation Bot added this to OpenELIS Community PR Priority List Aug 25, 2026

github-project-automation Bot moved this to Todo in OpenELIS Community PR Priority List Aug 25, 2026

pmanko mentioned this pull request Aug 25, 2026

feat(microbiology): add foundations and order routing (OGC-782) #3789

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pmanko changed the title ~~feat/782 ogc 782 microbiology mvp workbench ast~~ feat(microbiology): add case workbench and manual AST (OGC-782) Aug 25, 2026

pmanko mentioned this pull request Aug 25, 2026

feat(microbiology): add worklist and critical communication (OGC-782) #4135

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chatgpt-codex-connector Bot reviewed Aug 25, 2026

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pmanko force-pushed the feat/782-ogc-782-microbiology-mvp-workbench-ast branch from abf57b3 to 0b69229 Compare August 25, 2026 23:33

Copilot AI lite review requested due to automatic review settings August 25, 2026 23:33

Copilot started reviewing on behalf of pmanko August 25, 2026 23:35 View session

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pmanko force-pushed the feat/782-ogc-782-microbiology-mvp-workbench-ast branch 4 times, most recently from 9b740e5 to 6f2e90e Compare August 26, 2026 18:00

pmanko added 13 commits August 26, 2026 11:02

feat: add microbiology case workbench

78f08d4

docs: mark microbiology m4 PR task complete

aaa0958

feat: add microbiology manual AST

4dae8b5

docs: mark microbiology m5 PR task complete

af43e5c

fix(microbiology): complete case workbench and manual AST

8f5421c

fix(microbiology): keep workbench layer self-contained

e398359

fix(microbiology): complete workbench layer contracts

32e09bb

fix(microbiology): localize workbench enum labels

81b6d15

style(microbiology): format case controllers

d907285

fix(ci): preserve module errors and Playwright buckets

a1bcc9b

fix(microbiology): validate AST inputs and labels

b77dbee

fix(ci): skip Cypress binary in frontend images

9f2c95f

fix(microbiology): localize MALDI-TOF method

c54e9df

pmanko force-pushed the feat/782-ogc-782-microbiology-mvp-workbench-ast branch from 6f2e90e to c54e9df Compare August 26, 2026 18:08

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feat(microbiology): add case workbench and manual AST (OGC-782) - #4134

feat(microbiology): add case workbench and manual AST (OGC-782)#4134
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pmanko commented Aug 25, 2026 •

edited

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		private static final String DEFAULT_BREAKPOINT_AUTHORITY = "CLSI";
		private static final String DEFAULT_BREAKPOINT_VERSION = "2026";

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pmanko commented Aug 25, 2026 •

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