feat(microbiology): add WHONET export population filters

[pmanko]

Behavior delivered

• Adds combinable WHONET population filters for specimen type, organism,
  patient origin, and isolate significance using authoritative case data.
• Applies one normalized selection to both server-side preview and CSV
  generation, and stores that selection with the completed export record.
• Preserves the complete selection as canonical repeated query parameters so
  Configure and Preview can be bookmarked, reloaded, and shared.
• Places the single WHONET navigation entry under Reports while preserving the
  stable /Microbiology/whonet route and Reports breadcrumb.
• Uses a compact Carbon Configure -> Preview -> Generate workflow with filter
  funnel counts, all eligible AST readings, and exact mapping-repair links.
• Handles incomplete historical origin labels, empty reporting periods, and
  valid unidentified isolates without failing filter options or preview.

Product boundary

This slice does not infer screening or surveillance from Program, patient
origin, specimen, organism, location, or AMR eligibility. The next roadmap row
captures explicit Culture purpose as Clinical diagnosis/treatment or Active
screening/carriage, with historical missing data shown as Unspecified.

Export History, scheduling, AST-worklist and individual-case entry points,
advanced first-isolate policies, output-format qualification, and additional
readiness catalogs remain later M-09 roadmap slices. OpenELIS Work is
authoritative for workflow and visual intent.

Engineering notes

• Liquibase change 087-microbiology-whonet-export-selection.xml adds the one
  data-model field needed to retain export provenance and includes rollback.
• One typed selection and compiler drive filter options, preview, generation,
  and persisted provenance; there is no second filter implementation.
• Patient/sample context is batch-loaded through the existing worklist-context
  query rather than per-case service calls.
• Property-gated WHONET_FILTERS fixtures use authenticated application
  services only: no SQL seed, fixed primary key, DAO bypass, or production
  fixture endpoint exposure.
• Functional and video suites share one Playwright helper for canonical query
  construction, supported Carbon multi-select interaction, readiness, fixture
  labels, and CSV reading.

Verification

scripts/run-java21 mvn -Dtest=MicroWhonetDatasetServiceTest test
scripts/run-java21 mvn -Dtest=MicrobiologyUatScenarioServiceTest test
scripts/run-java21 mvn -Dtest=MicroWhonetPersistenceIntegrationTest,MicrobiologyWhonetExportSelectionLiquibaseTest,MicroWorklistContextHqlValidationTest,WHONetReportServiceMicrobiologyTest test
cd frontend && npm test -- --run src/components/microbiology/WhonetRoutes.test.js src/components/microbiology/WhonetService.test.js src/components/microbiology/__tests__/WhonetExport.test.jsx
BASE_URL=https://amr.openelis-global.org scripts/dev-stack playwright playwright/tests/foundational/core/microbiology-whonet-export.spec.ts
PLAYWRIGHT_MOBILE_EVIDENCE=on BASE_URL=https://amr.openelis-global.org scripts/dev-stack playwright --project=core-demo-video playwright/tests/demo/core/ogc-782-r9-whonet-export-filters.spec.ts

• Dataset service: 17/17 passed, including the unidentified-isolate regression.
• Deployed functional Playwright: shared auth and both journeys passed (3/3).
• Standard evidence project: shared auth plus desktop/mobile stories passed
  (3/3), producing five inspected screenshots and two titled MP4s.
• The Carbon interactions use the active listbox and Escape; there are no
  forced interactions or sleeps for test synchronization. Video-only pauses
  display title cards for human review.
• Code-qa R9 report

Stack and review evidence

• Native GitHub stack: this PR targets the open parent branch from
  PR #4097.
  OGC-788 Macro is a separate product stack and is not part of this PR's
  application scope; its current base relationship must be corrected
  independently before merge.
• Companion review-tooling change: PR #15.
• Authoritative mock: OpenELIS Work M-09.
• Live UAT source: AMR Review checklist, with distinct story AMR-S30.
• Deployment contract: AMR target.

Completion state

• Distinct R9 story is selectable in the live AMR Review overlay.
• Deployed foundational Playwright passes without WHONET server errors.
• Desktop/mobile screenshots were compared with the M-09 mock.
• Reproducible local evidence bundle created outside git for review.
• The R9 runtime behavior is deployed to AMR; public target health and smoke
  verification passed, and the deployed authenticated WHONET Playwright journey
  passed. The later roadmap-only commit changes no runtime behavior and is
  intentionally not deployed.
• Piotr validation, separate from technical merge readiness.

The Review button overlaps one filter in the full-page mobile screenshot. It is
external review-tooling chrome, not OpenELIS layout, and is not hidden with
application or evidence-only CSS.

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[Copilot]

Pull request overview

Adds combinable WHONET export population filters (specimen type, organism, patient origin, isolate significance) with a single normalized server-side query contract shared by preview and CSV generation, and relocates the WHONET navigation entry under Reports while preserving the stable /Microbiology/whonet route.

Changes:

• Backend: Normalize/export population filtering and expose period-scoped filter option endpoint used by UI.
• Frontend: Add Carbon multiselect filter controls that round-trip via deterministic repeated query params.
• Tests/docs: Update unit/integration/E2E coverage and align spec artifacts with the new filter slice.

Reviewed changes

Copilot reviewed 47 out of 47 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
volume/menu/menu_config.json	Moves WHONET menu entry under Reports and adjusts ordering.
src/main/java/org/openelisglobal/reports/service/WHONetReportService.java	Adds service API for filter-options retrieval.
src/main/java/org/openelisglobal/reports/service/WHONetReportServiceImpl.java	Implements filter-options retrieval as read-only transactional call.
src/main/java/org/openelisglobal/microbiology/controller/rest/MicroWhonetExportRestController.java	Adds /filter-options GET endpoint with authorization.
src/main/java/org/openelisglobal/microbiology/service/MicroWhonetDatasetService.java	Extends dataset service contract to include filter-options.
src/main/java/org/openelisglobal/microbiology/service/MicroWhonetDatasetServiceImpl.java	Applies combinable filters before deduplication; adds population loading + filter option derivation.
src/main/java/org/openelisglobal/microbiology/form/MicroWhonetExportQueryForm.java	Migrates population inputs to repeated-value lists (with single-value JSON compatibility).
src/main/java/org/openelisglobal/microbiology/form/MicroWhonetPreviewForm.java	Adds preview counters for each filter stage.
src/main/java/org/openelisglobal/microbiology/form/MicroWhonetFilterOptionsForm.java	New DTO for period-scoped filter choices.
src/main/java/org/openelisglobal/microbiology/form/MicroWhonetFilterOptionForm.java	New DTO for id/label option pairs.
src/main/java/org/openelisglobal/microbiology/dao/MicroCaseOrderDetailDAO.java	Adds DAO method to bulk load order details by case IDs.
src/main/java/org/openelisglobal/microbiology/dao/MicroOrganismDAO.java	Adds DAO method to bulk load organisms by IDs.
src/main/java/org/openelisglobal/microbiology/dao/MicroPatientOriginDAO.java	Adds DAO method to bulk load patient origins by codes.
src/main/java/org/openelisglobal/microbiology/daoimpl/MicroCaseOrderDetailDAOImpl.java	Implements bulk case-id lookup for order details.
src/main/java/org/openelisglobal/microbiology/daoimpl/MicroOrganismDAOImpl.java	Implements bulk organism lookup by IDs.
src/main/java/org/openelisglobal/microbiology/daoimpl/MicroPatientOriginDAOImpl.java	Implements bulk patient-origin lookup by codes.
src/main/java/org/openelisglobal/microbiology/service/MicrobiologyUatScenarioService.java	Provisions required sample status + report test section through services for scenario setup.
src/test/java/org/openelisglobal/reports/service/WHONetReportServiceMicrobiologyTest.java	Updates test query to use significance as list.
src/test/java/org/openelisglobal/microbiology/service/MicroWhonetDatasetServiceTest.java	Adds tests for combined filtering and period-scoped filter options; updates list-based significance.
src/test/java/org/openelisglobal/microbiology/controller/MicroWhonetExportRestControllerTest.java	Adds filter-options endpoint test; updates request binding expectations for repeated params.
src/test/java/org/openelisglobal/menu/util/MenuConfigurationLoaderTest.java	Asserts WHONET is exposed only under Reports and keeps stable URL.
src/test/java/org/openelisglobal/microbiology/service/MicrobiologyUatScenarioServiceTest.java	Adds tests for service provisioning of sample entered status and report test section.
src/test/java/org/openelisglobal/microbiology/MicroWhonetPersistenceIntegrationTest.java	Ensures sample type has WHONET code and updates list-based significance.
src/test/java/org/openelisglobal/microbiology/MicrobiologyReferenceDataIntegrationTest.java	Verifies fixture culture setup reuse for same method/workflow.
src/test/java/org/openelisglobal/microbiology/MicrobiologyOrderSaveIntegrationTest.java	Uses fixture helper that provisions an active sample type if missing.
src/test/java/org/openelisglobal/microbiology/fixture/MicrobiologyTestFixtures.java	Adds getOrCreateActiveSampleType and makes culture setup creation idempotent via service.
src/test/java/org/openelisglobal/microbiology/fixture/MicrobiologyTestFixturesTest.java	Adds unit test for provisioning active sample type via services (incl. localization).
src/test/java/org/openelisglobal/inventory/service/InventoryItemServiceTest.java	Adds assertion to ensure generated inventory IDs exceed fixture IDs.
src/test/java/org/openelisglobal/BaseWebContextSensitiveTest.java	Adds inventory item sequence mapping to avoid fixture/sequence collisions.
specs/782-ogc-782-microbiology-mvp-spec/tasks.md	Updates roadmap markers and records the filter slice + next culture-purpose slice.
specs/782-ogc-782-microbiology-mvp-spec/spec.md	Adds acceptance coverage for consistent filter application; clarifies terminology.
specs/782-ogc-782-microbiology-mvp-spec/data-model.md	Documents culture purpose field as follow-on model addition.
specs/782-ogc-782-microbiology-mvp-spec/evidence/code-qa-r9-2026-08-20.md	Adds QA evidence note for this slice.
specs/782-ogc-782-microbiology-m10-whonet-export/spec.md	Updates nav acceptance and adds follow-on stories/requirements for population and purpose.
specs/782-ogc-782-microbiology-m10-whonet-export/research.md	Adds research/ruling on clinical vs active screening culture purpose.
specs/782-ogc-782-microbiology-m10-whonet-export/plan.md	Updates plan for Reports-only nav and introduces R9 addendum for slice split.
frontend/src/languages/en.json	Adds i18n keys for filter labels, significance values, and filter-stage metrics.
frontend/src/components/microbiology/WhonetService.js	Serializes repeated filter params deterministically; adds filter-options fetch.
frontend/src/components/microbiology/WhonetService.test.js	Updates preview query serialization and adds filter-options request test.
frontend/src/components/microbiology/WhonetRoutes.js	Adds parsing/building of repeated population filters and legacy significance=ALL normalization.
frontend/src/components/microbiology/WhonetRoutes.test.js	Adds tests for round-tripping repeated filters and legacy ALL links.
frontend/src/components/microbiology/WhonetExport.scss	Adds filter grid styling and tightens layout toward operational compaction.
frontend/src/components/microbiology/WhonetExport.jsx	Adds multiselect filter UI backed by period-scoped filter options + preview metrics.
frontend/src/components/microbiology/tests/WhonetExport.test.jsx	Updates component tests for multiselect controls, canonical URL state, and list-based request.
frontend/playwright/tests/foundational/core/microbiology-whonet-export.spec.ts	Updates journeys to use Reports nav and validates filter preservation + metrics.
frontend/playwright/tests/demo/core/ogc-782-microbiology-whonet-export.spec.ts	Updates demo assertions for multiselect inclusion and mapping repair return flow.
frontend/playwright/helpers/seed-microbiology-data.ts	Extends seeding to set patient origin and significance for filter-focused fixtures.

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