Hipaa compliance

[Zacharyr41]

Summary

Complete HIPAA Security Rule compliance implementation for vcf-pg-loader, adding comprehensive security controls for handling Protected Health Information (PHI) in clinical genomics workflows.

Changes

Security Infrastructure

• Secrets Management (src/vcf_pg_loader/secrets.py): Secure credential handling with environment variable support, preventing password exposure in URLs/logs
• TLS Enforcement (src/vcf_pg_loader/tls.py): TLS 1.2+ required for all database connections with certificate validation (HIPAA 164.312(e)(1))

Audit Logging (HIPAA 164.312(b))

• Audit Schema (src/vcf_pg_loader/audit/): Partitioned audit tables with 6-year retention
• Immutability Triggers: Prevents modification/deletion of audit records
• Hash Chain Integrity: Cryptographic verification of audit log tampering
• CLI Commands: vcf-pg-loader audit verify, audit export, audit stats

Authentication & Access Control

• User Management (src/vcf_pg_loader/auth/): User authentication with bcrypt password hashing (HIPAA 164.312(d))
• Role-Based Access Control: Hierarchical roles with granular permissions (HIPAA 164.312(a)(1))
• Session Management: Configurable timeouts with automatic logoff (HIPAA 164.312(a)(2)(iii))
• CLI Commands: vcf-pg-loader auth, roles, permissions, session

PHI Protection

• PHI Detection (src/vcf_pg_loader/phi/): Pattern-based detection of SSN, MRN, names, dates, addresses
• Header Sanitization: Automatic removal of PHI from VCF headers during parsing
• Anonymization: k-anonymity and date generalization for de-identification (HIPAA 164.514(b))
• CLI Commands: vcf-pg-loader phi detect, phi anonymize, phi patterns

Data Security

• Encryption at Rest (src/vcf_pg_loader/data/encryption.py): AES-256-GCM for sensitive fields (HIPAA 164.312(a)(2)(iv))
• Secure Disposal (src/vcf_pg_loader/data/disposal.py): Two-person authorization, certificate of destruction (HIPAA 164.530(j))
• CLI Commands: vcf-pg-loader security, data dispose, data retention-report

Compliance Validation

• Compliance Checker (src/vcf_pg_loader/compliance/): Automated validation of all HIPAA controls
• Report Generation: JSON/HTML/text reports for compliance documentation
• CI Integration: GitHub Actions workflow for continuous compliance checking
• CLI Commands: vcf-pg-loader compliance check, compliance report, compliance status

Container Security

• Docker Hardening (src/vcf_pg_loader/doctor.py): Non-root user, read-only filesystem, dropped capabilities checks

New CLI Commands

Command	Description	HIPAA Reference
compliance check	Run all compliance checks	-
compliance report	Generate compliance report	-
compliance status	Quick compliance summary	-
audit verify	Verify audit log integrity	164.312(b)
audit export	Export audit logs	164.312(b)
auth create-user	Create authenticated user	164.312(d)
session list	List active sessions	164.312(a)(2)(iii)
roles create	Create RBAC role	164.312(a)(1)
phi detect	Scan for PHI	164.514(b)
phi anonymize	De-identify data	164.514(b)
security init	Initialize encryption	164.312(a)(2)(iv)
data dispose	Secure data disposal	164.530(j)

Test Coverage

• 76 new unit tests for compliance module
• Integration tests with PostgreSQL containers
• Tests for audit immutability, TLS, RBAC, session management
• PHI detection and anonymization tests

Files Changed

• 84 files changed, ~22,000 lines added
• New modules: audit/, auth/, phi/, data/, compliance/
• New workflows: compliance-check.yml

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🤖 Generated with Claude Code

[Zacharyr41]

This seems to adequately get the project to HIPAA compliance, or at least close enough so that when real PHI passes through these tools, the bulk of the work (>95% time coding) should be complete.