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Parthenon v1.0.5 — Data Quality & Validation

· 4 min read
Sanjay M. Udoshi MD
Creator, Parthenon

v1.0.5 — Data Quality & Validation​

v1.0.5 is the second stabilization release in the v1.0.x arc. With test infrastructure in place from v1.0.4, this release focuses on data integrity across the platform — programmatic audits that verify correctness of SQL generation, schema routing, vocabulary resolution, FHIR transformation, migration safety, and cross-schema referential integrity.

Why data quality matters​

Parthenon queries OMOP CDM data across 5 sources, each in its own PostgreSQL schema but sharing a single vocab schema for vocabulary. Every SQL template, every DQD check, every concept set resolution must correctly substitute the right schema name — a single hardcoded omop. in a template breaks silently for SynPUF, IRSF, Pancreas, and Eunomia. v1.0.5 adds programmatic guards that catch these issues automatically.

Achilles & DQD audit​

  • 128 Achilles SQL templates audited — every analysis verified for correct {@cdmSchema}, {@resultsSchema}, and {@vocabSchema} placeholder usage. No vocabulary tables using {@cdmSchema}, no hardcoded schema names, no unresolved placeholders. Zero violations found; test serves as regression guard.
  • 170+ DQD checks validated across all 5 CDM sources — each check's sqlTotal() and sqlViolated() verified for correct schema substitution with Acumenus (omop/vocab), SynPUF (synpuf/vocab), IRSF (irsf/vocab), Pancreas (pancreas/vocab), and Eunomia (eunomia/eunomia). 4,770 assertions.
  • Results schema routing validated — confirmed each source resolves to a distinct results schema (results, synpuf_results, irsf_results, pancreas_results, eunomia_results) with no collisions, and that SET search_path succeeds for each.

Vocabulary validation​

  • Solr index completeness command (solr:validate-vocabulary) — compares Solr vocabulary core document count against vocab.concept standard concepts, with spot-check sampling. Reports coverage % and exits non-zero if below 95%.
  • Concept set resolution schema audit — verified resolveToSql() generates correct vocab.concept_ancestor and vocab.concept_relationship references, uses singular OMOP table names, and correctly substitutes eunomia schema for the Eunomia demo source.

Ingestion & ETL validation​

  • Row count verification infrastructure — validated that PostLoadValidationService, ValidationResult, and IngestionJob have the correct method signatures, column schemas, and relationship wiring for end-to-end row count tracking through the pipeline.
  • FHIR-to-CDM transformation fidelity — 31 tests covering Patient (gender mapping to OMOP concept IDs, birth date parsing, US Core race/ethnicity extensions), Condition (SNOMED/ICD-10-CM mapping, onset/abatement dates), MedicationRequest (RxNorm mapping), Observation (category-based routing to measurement vs observation), and code system URI resolution.

Database integrity​

  • 242 migrations audited for idempotency — verified all have both up() and down() methods, no unsafe DROP TABLE without IF EXISTS in rollback, no $guarded = [] HIGHSEC violations. 3 advisory dropIfExists warnings in up() (all intentional cleanup migrations).
  • Cross-schema FK integrity validated — live queries against localhost PG17 verifying person.gender_concept_id, condition_concept_id, measurement_concept_id, and visit_occurrence.person_id all resolve to valid vocab.concept or person records. Finding: orphan drug_concept_ids in the 40213xxx range (SynPUF vocabulary version mismatch) — flagged as warning, investigation pending.
  • OMOP CDM CHECK constraints migration — adds 24 database-level CHECK constraints across 4 CDM schemas (omop, synpuf, irsf, pancreas) enforcing required fields: person gender/year_of_birth, visit/condition/drug start dates, and observation_period date ordering. Idempotent via DO/EXCEPTION.

OMOP Extension Bridge validation​

  • 1,715 imaging + 47 genomics records validated — read-only count verification of the OMOP extension bridge (image_occurrence, specimen, genomic_test, variant_occurrence, variant_annotation) and all app-layer xref tables. 10 Pest smoke tests for bridge model queryability.

By the numbers​

  • New test files: 11
  • New tests: 68
  • New assertions: 4,916
  • Achilles analyses audited: 128
  • DQD checks validated: 170+
  • CDM sources cross-validated: 5
  • Migrations audited: 242 (now 243)
  • CHECK constraints added: 24

Data quality finding​

The cross-schema FK audit discovered orphan drug_concept_id values in the 40213xxx range within omop.drug_exposure. These are SynPUF-era concept IDs that don't exist in the current vocab.concept table — a vocabulary version mismatch. This is flagged as a warning and will be resolved in a future vocabulary re-index or concept remapping pass.

Upgrade notes​

One new migration: 2026_04_11_000001_add_omop_cdm_check_constraints.php. Run php artisan migrate to apply the CHECK constraints. The migration is idempotent — safe to re-run.

New Artisan command: php artisan solr:validate-vocabulary for operational Solr index validation.

All other changes are test files — no API changes, no frontend changes, no breaking changes.

Contributors​

Claude Code + @sudoshi