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@amc-corey-cox amc-corey-cox released this 07 Apr 15:45
· 6 commits to main since this release
v1.2.0
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Architecture: LinkML-Map CLI Migration

The core transformation engine has been completely rewritten. map_data.py and the StreamWriter/MultiStreamWriter infrastructure have been removed (~1,300 lines deleted) and replaced with direct calls to linkml-map derive from the Makefile. This is the culmination of #275 and the most significant architectural change since v1.0.

  • Transformation specs are now composed at build time via compose_specs.py and passed directly to the linkml-map CLI
  • pipeline.Makefile gained significant new orchestration logic for spec composition and target schema handling
  • bdc-workflow.sh rewritten to support the new CLI-based flow, including --trans-spec for alternate spec repos
  • Integration tests rewritten with expanded assertions covering field values, cross-table derivations, unit conversions, and error handling
  • New unit tests for spec composition (test_compose_specs.py)

(#290, #296, closes #275, supersedes #253, #256)

Pipeline Behavior

  • Non-zero exit on mapping errors — pipeline now exits non-zero even in non-strict mode when mapping errors occur, making failures visible in CI and automation (#286)
  • Alternate trans-spec support — --trans-spec CLI flag allows specifying a different trans-spec repo/branch/path for testing against development specs (#296)

BDC Deployment

  • Three-tier container deployment — formalized dev → test → prod container registry separation. docker-dev for pipeline testing, docker-push-7bridges for data validation, bdc-v* tags for production releases (#298)
  • Seven Bridges API scripts — complete Python rewrite of task submission, monitoring, status checking, and log retrieval. Replaces ad-hoc bash scripts (#293)
  • Release process documented in RELEASING.md
  • Removed unused PyPI publish workflow (#298)

Toolchain & Dependencies

  • linkml-map 0.5.2 (from 0.4.0) — major version bump enabling CLI-based transformations
  • schema-automator 0.5.5 (from 0.5.4)
  • linkml 1.10.0 / linkml-runtime 1.10.0
  • Removed stale [tool.black] config and unused rstfmt/black dependencies

Testing & Data

  • MeasurementObservationSet added to toy data (#285)
  • Blood pressure transformation spec added to toy data for broader derivation coverage
  • Error spec test data for validating strict/non-strict error handling
  • Target schema added to toy data for CLI-based mapping
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