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Hard-cut Bloom to TapDB/EUID external reference model#178

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iamh2o merged 1 commit intomainfrom
codex/tapdb-euid-hard-cut
Mar 7, 2026
Merged

Hard-cut Bloom to TapDB/EUID external reference model#178
iamh2o merged 1 commit intomainfrom
codex/tapdb-euid-hard-cut

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@iamh2o iamh2o commented Mar 7, 2026

Summary

  • remove Bloom accessioning/package-kit workflow assets
  • enforce strict action execute payload and action-definition path
  • replace specimen atlas property blobs with explicit external reference objects
  • normalize Bloom Atlas lookup usage to integration lookup endpoints only

Validation

  • source bloom_activate.sh && pytest -q

@iamh2o iamh2o merged commit c1c3865 into main Mar 7, 2026
2 of 4 checks passed
@iamh2o iamh2o deleted the codex/tapdb-euid-hard-cut branch March 7, 2026 20:38
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Reviewed commit: 6c7422e265

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Comment on lines +1301 to +1304
handler_name = f"do_action_{action_name}"
handler = getattr(self, handler_name, None)
if not callable(handler):
raise Exception(f"Unknown action handler {handler_name}")

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P1 Badge Normalize action subtype before resolving handler

BloomObj.do_action now derives handler_name directly from the action key segment (parts[2]), but many action subtypes are hyphenated (for example plate-create-fill-auto in action configs), so this builds names like do_action_plate-create-fill-auto that cannot match the underscore-based Python methods (do_action_plate_create_fill_auto). In those cases execution now fails with Unknown action handler ..., which breaks a large set of existing actions at runtime.

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value = str(reference_value or "").strip()
if not value:
continue
validation_payload = atlas_validation.get(reference_type)

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P2 Badge Align validation lookup keys with Atlas reference types

_replace_external_references looks up validation metadata with atlas_validation.get(reference_type), but reference_type values are order_number/patient_id/shipment_number/kit_barcode while _validate_atlas_refs stores metadata under order/patient/shipment/testkit; this mismatch means each external reference is saved with empty validation payloads and loses provenance about Atlas freshness/cache status.

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