fix: mark cohort_definition_id as primary key in v5.3 and v5.4 (Fixes #787, #772)

[rtmalikian]

Fixes #787
Fixes #772

Problem

The cohort_definition_id field in the cohort_definition table is the natural primary key (each cohort definition has a unique ID), but it was not marked as isPrimaryKey=Yes in the CSV spec files for v5.3 and v5.4. The v6.0 CSV handles this differently (as a FK to the cohort table).

This means the generated DDL files for all database dialects (PostgreSQL, Oracle, SQL Server, BigQuery, etc.) are also missing the primary key constraint for the cohort_definition table in v5.3 and v5.4.

Solution

Changed isPrimaryKey from No to Yes for cohort_definition_id in the cohort_definition table in:

• inst/csv/OMOP_CDMv5.3_Field_Level.csv
• inst/csv/OMOP_CDMv5.4_Field_Level.csv

Updated all generated DDL primary key files (15 dialects × 2 versions = 30 files) to include the cohort_definition primary key constraint.

Updated the generated HTML documentation:

• docs/cdm53.html — Primary Key column now shows "Yes"
• docs/cdm54.html — Primary Key column now shows "Yes", and the cohort table's FK reference is correctly shown

Verification

# Verify CSV changes
grep "cohort_definition,cohort_definition_id" inst/csv/OMOP_CDMv5.3_Field_Level.csv
# Expected: ...Yes,integer,...,Yes,No,...
grep "cohort_definition,cohort_definition_id" inst/csv/OMOP_CDMv5.4_Field_Level.csv
# Expected: ...Yes,integer,...,Yes,No,...

# Verify DDL includes PK
grep "cohort_definition" inst/ddl/5.4/postgresql/OMOPCDM_postgresql_5.4_primary_keys.sql
# Expected: ALTER TABLE ... ADD CONSTRAINT xpk_cohort_definition PRIMARY KEY (cohort_definition_id);

Changelog

Date	Change	Author
2026-06-19	Mark cohort_definition_id as PK in v5.3/v5.4 CSVs, DDL, and HTML docs	rtmalikian

Files Changed

• inst/csv/OMOP_CDMv5.3_Field_Level.csv — isPrimaryKey No → Yes
• inst/csv/OMOP_CDMv5.4_Field_Level.csv — isPrimaryKey No → Yes
• inst/ddl/5.3/*/OMOPCDM_*_primary_keys.sql (15 files) — Added cohort_definition PK
• inst/ddl/5.4/*/OMOPCDM_*_primary_keys.sql (15 files) — Added cohort_definition PK
• docs/cdm53.html — Updated Primary Key column
• docs/cdm54.html — Updated Primary Key column + fixed cohort table FK display

Verification

• CSV grep confirms isPrimaryKey=Yes for cohort_definition_id
• DDL grep confirms PK constraint present in all dialects
• HTML docs show Primary Key=Yes in cohort_definition table

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About the Author: Raphael Malikian — Clinical AI Solutions Architect. I specialise in building and fixing AI/ML systems for healthcare, including vector databases, RAG pipelines, and clinical NLP. If you need help with your project or think I can add value to your organisation, feel free to reach out — I'd love to connect.

📧 rtmalikian@gmail.com
🔗 GitHub: https://github.com/rtmalikian
🔗 LinkedIn: http://www.linkedin.com/in/raphael-t-malikian-mbbs-bsc-hons-71075436a

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Disclosure: This code was developed with assistance from MiMo-v2.5-pro (Xiaomi) via Hermes Agent (Nous Research). All changes were reviewed, tested against the actual codebase, and verified for correctness.

[rtmalikian]

Friendly ping — this PR is ready for review. Happy to address any feedback!