BDMS-611: Implement Radionuclides backfill job and BDD step definitions

[kbighorse]

Summary

The feature spec tests/features/nma-chemistry-radionuclides-refactor.feature defines 7 scenarios for refactoring legacy NMA_Radionuclides rows into the Ocotillo Observation schema via a backfill job.

Current State

PR #573 (558-radionuclides-backfill) implements the full backfill job and BDD step definitions. Remaining work is resolving the local test DB setup (#585) and final review.

Completed

• Fix test harness — seed lexicon_term with required terms in before_all
• Implement step definitions — tests/features/steps/chemistry-backfill.py covering all 7 scenarios
• Implement backfill job — transfers/backfill/chemistry_backfill.py
  • Maps NMA_Radionuclides rows → Observation records keyed on nma_pk_chemistryresults (GlobalID)
  • Creates/reuses Parameter records by (parameter_name, matrix="water")
  • Sets detect_flag=false when Symbol = "<"
  • Stores Volume/VolumeUnit on the parent Sample (first-write-wins with conflict warnings)
  • Creates Notes records linked to observations
  • Preserves AnalysisMethod as-is (no lexicon mapping)
  • Skips orphan records (missing Sample linkage) and reports count
  • Is idempotent (re-run safe)
  • Deterministic row processing via ORDER BY NMA_Radionuclides.id
• Register in backfill orchestrator — wired into transfers/backfill/backfill.py
• CLI arg rejection — explicit error on removed --batch-size flag
• AnalysisMethod test cleanup scoped to test-created IDs (closes AnalysisMethod test cleanup should be scoped to test-created IDs #567)
• Chemistry backfill test cleanup handles errors gracefully (closes Chemistry backfill test cleanup should handle errors gracefully #566)

Remaining

• Resolve test DB setup so uv run pytest passes locally (Test DB setup should follow standard Python load_dotenv convention #585)
• Final code review and merge

Linked

• PR: feat: Radionuclides backfill job (#558) #573
• Jira: BDMS-611
• Blockers: Test DB setup should follow standard Python load_dotenv convention #585 (load_dotenv convention)
• Closes: AnalysisMethod test cleanup should be scoped to test-created IDs #567, Chemistry backfill test cleanup should handle errors gracefully #566
• Feature spec: tests/features/nma-chemistry-radionuclides-refactor.feature

[github-actions]

Linked Jira ticket created: BDMS-611