feat(microbiology): map WHONET specimen codes

[pmanko]

Stack

• Base: feat(microbiology): complete analyzer AST review and QC #4092
• Roadmap slice: OGC-782 R8 WHONET specimen mapping
• Review fixture dependency: DIGI-UW/openelis-review-tooling#15
• This PR is an official stacked PR and is intended to merge after its base PR.

Behavior contract

• Export the configured Sample Type WHONET specimen code rather than the local display label.
• Exclude only rows affected by a missing specimen code and report one exact, scoped warning.
• Open the owning Sample Type editor with the WHONET field focused.
• Return explicitly to the same canonical WHONET preview after saving.
• Keep mapped rows exportable when unrelated rows remain unmapped.
• Remove the competing generic WHONET terminology authoring path.
• Use a dedicated service-created UAT fixture with no SQL, fixed persisted IDs, or DAO bypass.

Implementation notes

• Reuses TypeOfSample.whonetCode as the single specimen mapping owner.
• Adds no schema change and no Liquibase migration.
• Preserves the existing long-format CSV contract.
• Splits the formerly coarse remaining WHONET roadmap into executable follow-on slices.
• Gives each service-created M4 scenario a distinct, schema-valid sample-type abbreviation. A real persistence integration test protects both uniqueness and the existing 10-character database constraint.

Validation

• Focused backend suite: 38 passed.
• Post-fix fixture/controller/dataset subset: 24 passed.
• Security subset: 6 passed.
• Real-schema fixture persistence integration: 1 passed.
• Focused frontend: 16 passed.
• Registered core-app Playwright: 2 passed locally and 2 passed against the deployed AMR target.
• Standard desktop demo/video: passed.
• Java Spotless, targeted formatting, and git diff --check: passed.
• Slice-level code-qa report: specs/782-ogc-782-microbiology-m10-whonet-export/evidence/code-qa-r8-2026-08-19.md.
• Repository-wide TypeScript still has pre-existing baseline errors; touched R8 files add zero errors.
• Review-tooling seed contract and repository contracts pass with AMR-S14:M4 in the official fixture manifest.

Deployment and UAT evidence

• AMR deployment: 20260820T030323Z-bca303b5be3d.
• Deployed application commit: bca303b5be3d586d62c5727f611f9042bf33dff3.
• Deployment health and smoke checks passed; / and /Microbiology/worklist returned 200.
• The official review-tooling seed successfully provisioned the AMR-S14 M4 fixture.
• Live registered Playwright proved the blocked preview, focused specimen repair, exact canonical return, partial eligibility, remaining organism warning, and two-row CSV with SPECIMEN_TYPE=BLD.
• Grist AMR-S14 is version 2.0 with seven required, ordered reviewer steps. The live Review overlay shows the story, full context, and deployed application SHA.
• PR head 32a09dfb9 adds only roadmap/evidence closure after the deployed runtime commit, so it was intentionally not redeployed.

The external evidence bundle contains a 39-second H.264 MP4 and five stable screenshots covering configure, blocked preview, focused specimen repair, retained organism warning, and CSV generation.

Current check state

GitHub's backend and frontend checkpoints are red as of this update, so this PR is not merge-ready yet. Focused local and deployed validation passed, but that does not override required CI. The failed backend job did not expose failed-step logs through gh; this needs one grounded CI diagnosis rather than repeated polling.

Separate issue observed

Fresh scripts/dev-stack up can lose an analyzer-mock create request while attaching the mock container to the network, then poll for an analyzer that was never created. The core OpenELIS stack remains healthy and the defect is unrelated to this WHONET slice; it is recorded in the code-qa report rather than patched here.

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[Copilot]

Pull request overview

Implements the R8 WHONET specimen mapping slice by exporting TypeOfSample.whonetCode (instead of the local specimen label), excluding only rows with missing specimen codes, and providing an exact repair/return path via Sample Type Management while removing WHONET as a parallel generic terminology authoring source.

Changes:

• Backend WHONET dataset generation now projects TypeOfSample.whonetCode into SPECIMEN_TYPE and excludes unmapped specimen rows with a scoped warning pointing at the owning Sample Type.
• Sample Type admin flow now supports WHONET-focused repair + return-to-preview navigation; WHONET is removed from generic terminology sources.
• Test coverage expanded across unit, security slice, persistence integration, and Playwright (foundational + demo) to protect the mapping/repair contract and schema constraints.

Reviewed changes

Copilot reviewed 22 out of 22 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
src/main/java/org/openelisglobal/microbiology/service/MicroWhonetDatasetServiceImpl.java	Excludes isolates missing specimen WHONET code; projects specimen WHONET code + warning metadata into preview/export.
src/main/java/org/openelisglobal/microbiology/service/MicrobiologyUatScenarioService.java	Ensures WHONET UAT scenarios create a “pending specimen mapping” sample type and keeps the base UAT sample type mapped.
src/main/java/org/openelisglobal/common/management/controller/rest/SampleTypeManagementRestController.java	Removes WHONET from allowed terminology sources while allowing unchanged legacy WHONET mappings to round-trip.
src/test/java/org/openelisglobal/microbiology/service/MicroWhonetDatasetServiceTest.java	Adds unit tests asserting mapped specimen export and scoped exclusion/warning for unmapped specimen codes.
src/test/java/org/openelisglobal/microbiology/service/MicrobiologyUatScenarioServiceTest.java	Verifies multiple M4 scenarios provision distinct schema-valid sample types and pending mappings through services.
src/test/java/org/openelisglobal/microbiology/MicroWhonetPersistenceIntegrationTest.java	Adds persistence integration coverage to enforce distinct sample types + abbreviation constraints through real schema/service.
src/test/java/org/openelisglobal/common/management/controller/rest/SampleTypeManagementRestControllerSecurityTest.java	Adds security-slice coverage preventing WHONET as a terminology source while supporting legacy mapping preservation.
frontend/src/components/microbiology/WhonetRoutes.js	Adds specimen-type repair URL generation with validated local returnTo preservation.
frontend/src/components/microbiology/WhonetRoutes.test.js	Tests specimen repair URL composition and rejection of external return destinations.
frontend/src/components/microbiology/WhonetExport.jsx	Renders “Fix specimen mapping” links using canonical return URL state.
frontend/src/components/microbiology/tests/WhonetExport.test.jsx	Verifies specimen-mapping warning links point to Sample Type editor with exact preview return.
frontend/src/components/admin/sampleTypeManagement/SampleTypeManagement.jsx	Adds WHONET code field + focus-on-repair + explicit return link after save.
frontend/src/components/admin/sampleTypeManagement/SampleTypeManagement.test.jsx	Tests WHONET-focused repair flow: focus, save payload, and exact return navigation.
frontend/src/components/admin/sampleTypeManagement/sections/TerminologySection.jsx	Removes WHONET from selectable generic terminology sources.
frontend/src/languages/en.json	Adds i18n strings for WHONET specimen code field, helper text, return link, and specimen repair action.
frontend/playwright/helpers/seed-microbiology-data.ts	Extends WHONET export seed contract to include sampleTypeId for repair navigation.
frontend/playwright/tests/foundational/core/microbiology-whonet-export.spec.ts	Foundational E2E validates blocked preview → specimen repair → exact return → CSV includes SPECIMEN_TYPE=BLD.
frontend/playwright/tests/demo/core/ogc-782-microbiology-whonet-export.spec.ts	Demo flow updated to record specimen repair and canonical return before remaining organism mapping gap.
specs/782-ogc-782-microbiology-mvp-spec/tasks.md	Splits WHONET roadmap into smaller follow-on slices; marks specimen-mapping slice complete.
specs/782-ogc-782-microbiology-m10-whonet-export/spec.md	Documents follow-on story and requirements for mapped specimen codes and repair/return behavior.
specs/782-ogc-782-microbiology-m10-whonet-export/plan.md	Adds R8 engineering addendum describing reuse of TypeOfSample.whonetCode and removal of WHONET terminology source.
specs/782-ogc-782-microbiology-m10-whonet-export/evidence/code-qa-r8-2026-08-19.md	Adds R8 code-QA evidence and validation summary.

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