Add uuid5 identifiers to all FHS-ingest YAML files by amc-corey-cox · Pull Request #359 · RTIInternational/NHLBI-BDC-DMC-HV

amc-corey-cox · 2026-02-20T16:03:37Z

Summary

Adds deterministic uuid5 identifiers to all FHS-ingest YAML files so Visit and Observation/Condition/Demography records can be linked by matching UUIDs computed from participant_id + visit_name
visit.yaml: Adds id slot with uuid5 expr to all 35 Visit blocks (including 3 SHHS blocks with distinct participant PHV fields)
121 observation/condition/demography files: Transforms associated_visit from name:/value_mappings: to uuid5 expr: (1,771 static name + 373 value_mappings blocks)
18 pht006027 blocks with associated_participant: value: UNKNOWN left unchanged (no participant PHV available)

uuid5 patterns

Static name (most common):

# Before:
associated_visit:
  name: FHS OFFSPRING EXAM 2
  range: string
# After:
associated_visit:
  expr: 'uuid5("https://w3id.org/bdchm/Visit", str({phv00008379}) + ":FHS OFFSPRING EXAM 2")'

Value mappings:

# Before:
associated_visit:
  populated_from: phv00277016
  value_mappings:
    '2': FHS NEW OFFSPRING SPOUSE EXAM 1
    '3': FHS GENERATION 3 EXAM 1
# After:
associated_visit:
  expr: 'uuid5("...", str({phv00277015}) + ":" + case(({phv00277016} == ''2'', ''FHS NEW...''), ...))'

Visit id (visit.yaml only):

# Added before existing name:
id:
  expr: 'uuid5("https://w3id.org/bdchm/Visit", str({phv00177926}) + ":" + <name_expr>)'
name:
  expr: '<existing case expr>'

Verification performed

All 2,584 PHV references in uuid5 expressions verified to already exist in original blocks (zero new PHVs introduced)
All PHVs used as local references (consistent with original populated_from usage)
All 124 files pass yaml.safe_load() validation
Block counts preserved in every file

Pre-existing data quality issues found during review

Cross-referencing visit names between observation files and visit.yaml revealed several pre-existing issues (not introduced by this PR) that are tracked in separate issues.

Test plan

Verify uuid5 expressions parse correctly in linkml-map transformer
Run FHS-ingest temporal pipeline end-to-end
Spot-check that Visit id values match associated_visit values for same participant + visit combination

🤖 Generated with Claude Code

Regenerate uuid5 transformation on top of v35 (PR #358). Adds deterministic Visit identifiers for longitudinal linking: - Type A (1771 blocks): static visit value → uuid5 expr - Type B (373 blocks): value_mappings → uuid5 + case() expr - Type C (35 blocks): visit.yaml id field insertion Blocks with UNKNOWN participant are left unchanged. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

amc-corey-cox · 2026-02-25T19:30:35Z

Regenerated on v35 (force-push)

Branch has been force-pushed with uuid5 identifiers regenerated on top of the v35 files from PR #358. The previous v33 uuid5 state has been preserved in the release repo.

Changes from previous version

Built on v35 base (PR Mapping FHS new version updated - moving from v33 to v35 #358 merged) instead of v33
PHV numbers updated to match v35 mappings
value: field (v35) instead of name: field (v33) for static visit names

Transformation summary

Type A (static value → uuid5 expr): 1,771 blocks
Type B (value_mappings → uuid5 + case() expr): 373 blocks
Type C (visit.yaml id insertion): 35 blocks
Total: 2,179 transformations across 122 files

Validation

All files pass validate_ingest_yamls.py (linkml-map schema validation)
5,801 blocks validated across 606 files
Only 3 pre-existing known issues (manifest, empty il18, pr_qrs_qt nesting)

Copilot

Pull request overview

Adds deterministic uuid5-based Visit identifiers across FHS-ingest YAML transforms so Visit and Observation/Condition/Demography records can be linked via uuid5(participant_id + ":" + visit_name).

Changes:

Replaces many associated_visit value / value_mappings blocks with expr: uuid5(...) expressions.
Updates several multi-visit mapping cases to compute visit UUIDs deterministically from participant + mapped visit name.
Keeps existing block structure while changing visit-linking representation.

Reviewed changes

Copilot reviewed 108 out of 122 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
priority_variables_transform/FHS-ingest/tak_med_diab.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/tak_insulin.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/tak_angiorecepblk.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/tak_alphablk.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/tak_aldorecepblk.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/tak_aceinhib.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/stroke.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/spo2.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/sodium_intak.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/sodium_blood.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/sleep_duration_daily.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/rdw.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/rdbld_ct.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/qt_ekg.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/pr_qrs_qt.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/pmv.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/platelet_ct.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/pad.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/opg.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/obesity.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/nt_bnp.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/mpo.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/monocyte_ncnc_bld.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/mmp9.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/mean_art_press.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/mcv.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/mcp1.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/mchc.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/mch.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/lympho_pct.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/lactate_dehyd.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/lactate.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/insulin_in_blood.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/il6.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/il1_beta.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/il10.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/icam.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/hypertension.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/hist_cvd.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/hist_cor_bypg.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/hist_cor_angio.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/hemo_a1c.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/hemo.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/hemat.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/fvc.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/fruit_serving.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/fibrin.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/fev1.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/ferritin.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/fast_lipids.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/fast_gluc_bld.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/fam_stroke.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/fam_income.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/factor_8.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/factor_7.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/eselectin.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/eosinophil_ncnc_bld.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/edu_lvl.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/demography.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/d_dimer.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/cysc_bld.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/crp.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/creat_urin.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/copd.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/chloride_bld.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/cesd_score.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/cd40.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/carotid_sten_right.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/carotid_sten_left.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/carotid_imt.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/cac_volume.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/cac_score.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/bun.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/bnp.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/bmi.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/bilirubin_tot.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/bilirubin_con.yaml	Convert `associated_visit` constants to uuid5 `expr`
priority_variables_transform/FHS-ingest/basophil_ncnc_bld.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/ast_sgot.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/apnea_hypop_index.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/angina.yaml	Convert `associated_visit` mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/alt_sgpt.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/albumin_urine.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/albumin_bld.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`
priority_variables_transform/FHS-ingest/afib.yaml	Convert `associated_visit` constants/mappings to uuid5 `expr`

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priority_variables_transform/FHS-ingest/tak_med_diab.yaml

priority_variables_transform/FHS-ingest/platelet_ct.yaml

priority_variables_transform/FHS-ingest/lactate_dehyd.yaml

priority_variables_transform/FHS-ingest/hemat.yaml

priority_variables_transform/FHS-ingest/ast_sgot.yaml

priority_variables_transform/FHS-ingest/eosinophil_ncnc_bld.yaml

priority_variables_transform/FHS-ingest/fvc.yaml

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

This was referenced Feb 20, 2026

FHS-ingest: Concept codes used as associated_visit names in hypertension.yaml #360

Open

FHS-ingest: Missing Visit blocks for sub-study and non-standard visits #361

Open

amc-corey-cox force-pushed the add-uuid5-fhs-ingest branch from becddec to 34ee0af Compare February 25, 2026 19:28

amc-corey-cox requested a review from Copilot February 25, 2026 19:31

Copilot AI reviewed Feb 25, 2026

View reviewed changes

Fix OFFFSPRING typo in fvc.yaml uuid5 expression

875f513

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

amc-corey-cox merged commit d6a08ea into main Feb 25, 2026
1 check passed

amc-corey-cox deleted the add-uuid5-fhs-ingest branch February 25, 2026 20:11

amc-corey-cox restored the add-uuid5-fhs-ingest branch February 25, 2026 20:12

This was referenced Feb 25, 2026

FHS-ingest: malformed age_at_observation expressions in multi-visit blocks #363

Open

Fix v35 participant PHV regression in FHS-ingest #364

Merged

QA issues found in FHS-ingest update #367

Open

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Add uuid5 identifiers to all FHS-ingest YAML files#359

Add uuid5 identifiers to all FHS-ingest YAML files#359
amc-corey-cox merged 2 commits intomainfrom
add-uuid5-fhs-ingest

amc-corey-cox commented Feb 20, 2026

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amc-corey-cox commented Feb 25, 2026

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amc-corey-cox commented Feb 20, 2026

Summary

uuid5 patterns

Verification performed

Pre-existing data quality issues found during review

Test plan

Uh oh!

amc-corey-cox commented Feb 25, 2026

Regenerated on v35 (force-push)

Changes from previous version

Transformation summary

Validation

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