feat: Radionuclides backfill job (#558) by kbighorse · Pull Request #573 · DataIntegrationGroup/OcotilloAPI

kbighorse · 2026-02-28T04:07:26Z

Summary

Implements the Radionuclides backfill pipeline that maps NMA_Radionuclides → Observation records with chemistry metadata
Adds Alembic migration for new columns on observation (nma_pk_chemistryresults, detect_flag, uncertainty, analysis_agency) and sample (nma_pk_chemistrysample, volume, volume_unit)
Drops stale thing_id FK from NMA_Radionuclides (relationships now go through NMA_Chemistry_SampleInfo)
Adds BDD test suite (7 scenarios) covering happy path, idempotency, orphan handling, edge cases
Adds pCi/L unit and Chemistry Observation note type to lexicon

Robustness

Per-row savepoint isolation — one bad row never aborts the run
Rows with missing AnalysisDate are skipped (logged as errors) instead of using sentinel values
Migration upgrade is idempotent (checks information_schema before dropping columns/FKs)
Migration downgrade safely restores thing_id (nullable → backfill → NOT NULL)
Full tracebacks logged via logger.exception() for per-row failures

Test safety

Cleanup scoped to scenario sample_ids (no global deletes)
Analysis method tracking scoped to scenario samples

Closes #558
Refs #565, #566, #567, #568, #570, #571

Test plan

CI passes (BDD scenarios + existing pytest suite)
Run alembic upgrade head on a fresh DB — migration applies cleanly
Run alembic downgrade -1 — migration rolls back cleanly
Run backfill against staging NMA_Radionuclides data
Verify idempotency: re-running backfill produces 0 inserts, 0 errors

🤖 Generated with Claude Code

Add chemistry backfill that maps legacy NMA_Radionuclides rows into Observation records keyed on nma_pk_chemistryresults (idempotent upsert). - Schema: add chemistry columns to Observation and Sample models/schemas - Migration: add columns + unique constraints, drop stale NMA_Radionuclides.thing_id - Lexicon: add pCi/L unit and Chemistry Observation note type - Backfill: resolve Samples via nma_pk_chemistrysample, create Parameters, AnalysisMethods, Notes; detect_flag from legacy Symbol qualifier - Tests: BDD step definitions for all 7 scenarios, feature file fixes - Orchestrator: wire radionuclides step into backfill pipeline Refs #558 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Wrap cleanup chain in try/except to prevent orphan data on failure (#566) - Scope AnalysisMethod cleanup to test-created IDs only (#567) Also addresses #565 (scalar_one hardening) and #568 (remove unused parameter_ids tracker) which were applied to the new files in the preceding feature commit. Refs #558 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add per-row savepoint isolation so one bad row doesn't abort the run - Skip rows with missing AnalysisDate instead of inserting epoch sentinel - Remove unused batch_size parameter from backfill signatures and CLI - Fix migration downgrade to backfill thing_id before setting NOT NULL - Track analysis_method_ids in test step defs for scoped cleanup Refs #558 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…leanup - Migration upgrade now checks information_schema before dropping thing_id column, guarding against environments where it was already removed - run_backfill.sh no longer references removed --batch-size parameter - Test observation cleanup scoped to scenario sample_ids instead of blanket nma_pk_chemistryresults IS NOT NULL query Refs #558, #570 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

… tracking - Migration upgrade dynamically discovers FK names via sa.inspect() with guard for missing name entries - Per-row exception handler now logs full traceback via logger.exception() before appending summary to result.errors - Analysis method tracking scoped to scenario sample_ids - Removed incorrect issue reference from test comment Refs #558 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Implements a radionuclides chemistry backfill pipeline that converts legacy NMA_Radionuclides rows into the Ocotillo Observation schema (plus related Sample metadata), wires it into the backfill orchestrator, and adds BDD coverage + schema/migration/lexicon updates needed to support the new fields.

Changes:

Added a radionuclides backfill implementation with per-row savepoints, idempotent upserts, and Notes creation.
Added DB/schema support for chemistry audit keys + metadata (nma_pk_chemistryresults, detect_flag, uncertainty, analysis_agency, nma_pk_chemistrysample, volume, volume_unit) via Alembic + models + API schemas.
Added/updated BDD steps and test cleanup logic; extended lexicon with pCi/L and Chemistry Observation.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
`transfers/backfill/chemistry_backfill.py`	Implements the radionuclides backfill (Sample resolution, Observation upsert, volume + Notes handling).
`transfers/backfill/backfill.py`	Registers the radionuclides backfill in the orchestrator and improves logging/output.
`tests/features/steps/chemistry-backfill.py`	Adds Behave step definitions and helpers for radionuclides backfill scenarios.
`tests/features/nma-chemistry-radionuclides-refactor.feature`	Minor scenario adjustments for radionuclides backfill BDD feature.
`tests/features/environment.py`	Adds per-scenario cleanup for chemistry backfill fixtures.
`db/sample.py`	Adds chemistry audit/sample metadata columns to the ORM model.
`db/observation.py`	Adds chemistry audit + metadata columns to the ORM model.
`schemas/sample.py`	Exposes new Sample chemistry fields in the API response schema.
`schemas/observation.py`	Exposes new Observation chemistry fields in the API response schema.
`alembic/versions/545a5b77e5e8_add_chemistry_backfill_columns_to_.py`	Migration adding columns/constraints and dropping legacy `thing_id` from `NMA_Radionuclides`.
`core/lexicon.json`	Adds lexicon terms for `pCi/L` and `Chemistry Observation`.
`run_backfill.sh`	Updates backfill runner invocation to match the orchestrator CLI changes.

tests/features/steps/chemistry-backfill.py

transfers/backfill/chemistry_backfill.py

alembic/versions/545a5b77e5e8_add_chemistry_backfill_columns_to_.py

tests/features/steps/chemistry-backfill.py

…ow catch - Volume/volume_unit test assertions query by scenario sample_ids - existing_keys set lowercases DB values to match global_id_str normalization - Per-row catch broadened to Exception with logger.exception() for tracebacks - Analysis method tracking scoped to scenario samples - Migration FK drop guarded against missing name entries - Resolve stash merge conflicts in sample volume steps Refs #558 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

jirhiker

Looks good from the description. @ksmuczynski should review re database schema

ksmuczynski · 2026-03-02T16:26:47Z

@jirhiker @kbighorse Great, thanks. Will take a closer look as soon as the well inventory ingestion work is completed.

Copilot

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 2 comments.

tests/features/steps/chemistry-backfill.py

tests/features/environment.py

Snapshot AnalysisMethod IDs before/after backfill to track only actually-created methods, preventing deletion of pre-existing rows. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Delete context._backfill_created in finally block to prevent ID accumulation across scenarios causing redundant deletes. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Add ORDER BY id to legacy query so lowest-PK row wins when multiple radionuclide rows map to the same Sample (volume/volume_unit) - Skip overwrites with warning when a conflict is detected - Reject unknown CLI args in backfill entrypoint instead of silently ignoring them Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…backfill

…ntegrationGroup/OcotilloAPI into 558-radionuclides-backfill

Skip pg_cron extension creation gracefully when unavailable instead of hard-failing, unblocking local dev and test environments. Refs #576 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot

Pull request overview

Copilot reviewed 14 out of 14 changed files in this pull request and generated no new comments.

Skip pg_cron extension creation gracefully when unavailable instead of hard-failing, unblocking local dev and test environments. Also skip search vector trigger sync for tables that don't exist yet (e.g. asset) to avoid NoSuchTableError during test setup. Refs #576 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

…ntegrationGroup/OcotilloAPI into 558-radionuclides-backfill

kbighorse and others added 4 commits February 27, 2026 19:37

Copilot AI review requested due to automatic review settings February 28, 2026 04:07

kbighorse and others added 2 commits February 27, 2026 20:07

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kbighorse review requested due to automatic review settings February 28, 2026 08:45

kbighorse and others added 2 commits February 28, 2026 00:46

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kbighorse self-assigned this Feb 28, 2026

kbighorse requested a review from jirhiker February 28, 2026 09:21

jirhiker requested a review from ksmuczynski March 2, 2026 16:19

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Merge branch 'staging' into 558-radionuclides-backfill

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tests/features/steps/chemistry-backfill.py Outdated Show resolved Hide resolved

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kbighorse and others added 4 commits March 2, 2026 09:36

fix(tests): scope analysis method cleanup to only backfill-created rows

ac44f6b

Snapshot AnalysisMethod IDs before/after backfill to track only actually-created methods, preventing deletion of pre-existing rows. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

fix(tests): clear backfill tracking after scenario cleanup

10f3e41

Delete context._backfill_created in finally block to prevent ID accumulation across scenarios causing redundant deletes. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Formatting changes

ae60c1f

Copilot AI review requested due to automatic review settings March 2, 2026 18:29

kbighorse review requested due to automatic review settings March 2, 2026 18:29

kbighorse added 2 commits March 2, 2026 10:35

Merge remote-tracking branch 'origin/staging' into 558-radionuclides-…

243f5cf

…backfill

Merge branch '558-radionuclides-backfill' of https://github.com/DataI…

f7cef22

…ntegrationGroup/OcotilloAPI into 558-radionuclides-backfill

fix: make pg_cron optional for local development

09c31ff

Skip pg_cron extension creation gracefully when unavailable instead of hard-failing, unblocking local dev and test environments. Refs #576 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Copilot AI review requested due to automatic review settings March 2, 2026 19:37

Copilot started reviewing on behalf of kbighorse March 2, 2026 19:38 View session

Copilot AI reviewed Mar 2, 2026

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kbighorse and others added 2 commits March 2, 2026 12:40

Merge branch '558-radionuclides-backfill' of https://github.com/DataI…

0acbfb6

…ntegrationGroup/OcotilloAPI into 558-radionuclides-backfill

kbighorse assigned ksmuczynski and unassigned kbighorse Mar 4, 2026

kbighorse mentioned this pull request Mar 4, 2026

BDMS-611: Implement Radionuclides backfill job and BDD step definitions #558

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feat: Radionuclides backfill job (#558)#573

feat: Radionuclides backfill job (#558)#573
kbighorse wants to merge 18 commits intostagingfrom
558-radionuclides-backfill

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kbighorse commented Feb 28, 2026

Summary

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