BIO-QMS Admin & Compliance Documentation

Version: 1.0.0 Last Updated: 2026-02-17 Regulatory Scope: FDA 21 CFR Part 11, HIPAA, SOC 2, EU Annex 11 Platform: BIO-QMS Regulated SaaS Quality Management System

Document Purpose

This comprehensive reference provides:

System Administrator Guide - User management, SSO, system configuration, troubleshooting
Compliance Officer Guide - Audit review, regulatory procedures, evidence collection
Validation Protocol Documentation - IQ/OQ/PQ templates and execution procedures
Regulatory Submission Package - FDA CSV documentation and submission templates

Target Audience:

System Administrators managing BIO-QMS installations
Compliance Officers ensuring regulatory adherence
Validation Engineers executing qualification protocols
Quality Assurance teams preparing regulatory submissions
IT Security personnel managing access controls
Auditors reviewing system compliance

System Administrator Guide
- 1.1 User Management
- 1.2 Role Configuration
- 1.3 Organization Settings
- 1.4 SSO Setup (SAML 2.0, OIDC)
- 1.5 API Key Management
- 1.6 Backup and Recovery
- 1.7 Troubleshooting
Compliance Officer Guide
- 2.1 Audit Trail Review
- 2.2 Compliance Dashboards
- 2.3 FDA Part 11 Procedures
- 2.4 HIPAA Procedures
- 2.5 SOC 2 Procedures
- 2.6 Evidence Collection
- 2.7 Compliance Report Generation
Validation Protocol Documentation
- 3.1 IQ Protocol (Installation Qualification)
- 3.2 OQ Protocol (Operational Qualification)
- 3.3 PQ Protocol (Performance Qualification)
- 3.4 Execution Procedures
- 3.5 Evidence Packaging
Regulatory Submission Documentation
- 4.1 FDA CSV Package
- 4.2 System Description
- 4.3 Risk Assessment
- 4.4 Validation Summary
- 4.5 EU Annex 11 Submissions

1. System Administrator Guide

1.1 User Management

1.1.1 User Lifecycle Management

Creating New Users

# Via Admin UI
1. Navigate to: Admin → User Management → Create User
2. Required fields:
   - Email (must be unique, validates against domain whitelist)
   - First Name / Last Name
   - Organization assignment
   - Initial role(s)
   - Department (optional)
3. Select authentication method:
   - SSO (SAML/OIDC) - recommended for enterprises
   - Email/Password - requires strong password policy compliance
4. Set account status: Active | Pending | Suspended
5. Configure MFA requirement (recommended for privileged accounts)
6. Review and create

# Via API (for bulk operations)
POST /api/v1/users
Content-Type: application/json
Authorization: Bearer {ADMIN_API_KEY}

{
  "email": "john.doe@pharma.com",
  "firstName": "John",
  "lastName": "Doe",
  "organizationId": "org_abc123",
  "roles": ["QA_REVIEWER"],
  "department": "Quality Assurance",
  "requireMFA": true,
  "authMethod": "SSO"
}

User Status States

Status	Description	Can Login	Audit Trail
Active	Full access granted	Yes	All actions logged
Pending	Awaiting activation/verification	No	Creation logged
Suspended	Temporarily disabled	No	Suspension reason required
Locked	Security lockout (failed auth)	No	Auto-unlock after timeout
Deactivated	Permanently disabled	No	Cannot be reactivated

Bulk User Import

# CSV format for bulk import
# File: users_import.csv
email,firstName,lastName,organizationId,roles,department
jane.smith@pharma.com,Jane,Smith,org_abc123,QA_MANAGER,Quality
bob.jones@pharma.com,Bob,Jones,org_abc123,DOCUMENT_AUTHOR,Operations

# Import via CLI tool
./bio-qms-admin import-users --file users_import.csv --send-invites

# Validation checks performed:
- Email format and uniqueness
- Organization exists
- Roles are valid
- Duplicate detection

1.1.2 Password Policy Configuration

Policy Settings (Admin → Security → Password Policy)

password_policy:
  minimum_length: 12
  require_uppercase: true
  require_lowercase: true
  require_numbers: true
  require_special_characters: true
  special_characters: "!@#$%^&*()_+-=[]{}|;:,.<>?"

  # Password history
  prevent_reuse_count: 10  # Last 10 passwords cannot be reused

  # Expiration
  max_age_days: 90
  expiration_warning_days: 14

  # Lockout policy
  max_failed_attempts: 5
  lockout_duration_minutes: 30
  lockout_reset_method: "admin_or_timeout"

  # Complexity rules
  min_unique_characters: 8
  prohibit_common_passwords: true
  prohibit_user_info: true  # No name, email parts

  # Multi-factor authentication
  mfa_enforcement: "role_based"  # all | role_based | optional
  mfa_required_roles: ["ADMIN", "QA_MANAGER", "VALIDATOR"]

Compliance Mapping

FDA 21 CFR Part 11.300(b): Use of secure, computer-generated, time-stamped audit trails
HIPAA: Unique user identification (§164.312(a)(2)(i))
SOC 2 CC6.1: Logical access controls including password requirements

1.1.3 User Deactivation Process

Offboarding Checklist

## User Deactivation Procedure

**Trigger Events:**
- Employee termination
- Role change removing system access
- Security incident
- Extended leave (optional suspension vs. deactivation)

**Steps:**

1. **Pre-Deactivation** (perform before account disable)
   - [ ] Transfer document ownership to successor
   - [ ] Reassign active tasks and approvals
   - [ ] Archive personal workspace items
   - [ ] Export user-specific reports (if required)
   - [ ] Review open e-signature workflows

2. **Deactivation** (immediate upon authorization)
   - [ ] Set user status to "Deactivated"
   - [ ] Revoke all active sessions (force logout)
   - [ ] Disable API keys associated with user
   - [ ] Remove from active role assignments
   - [ ] Document deactivation reason in audit log

3. **Post-Deactivation** (within 24 hours)
   - [ ] Verify no orphaned permissions remain
   - [ ] Confirm audit trail integrity (all past actions preserved)
   - [ ] Notify relevant stakeholders (QA manager, compliance)
   - [ ] Update access control matrix
   - [ ] File deactivation certificate in personnel records

4. **Data Retention** (permanent)
   - User record: Retained indefinitely (audit trail integrity)
   - Audit logs: Per retention policy (typically 7+ years)
   - E-signatures: Retained with signed documents (FDA requirement)
   - Personal data: Anonymize per GDPR if applicable

Deactivation API Call

PATCH /api/v1/users/{userId}/deactivate
Authorization: Bearer {ADMIN_API_KEY}

{
  "reason": "Employment termination",
  "effectiveDate": "2026-02-17T17:00:00Z",
  "transferOwnershipTo": "user_xyz789",
  "retainAuditTrail": true,  # Always true for compliance
  "notifyCompliance": true
}

1.2 Role Configuration

1.2.1 Built-in Roles

Standard Role Hierarchy

SYSTEM_ADMIN (highest privilege)
├── ORG_ADMIN
│   ├── QA_MANAGER
│   │   ├── QA_REVIEWER
│   │   └── VALIDATOR
│   ├── DOCUMENT_MANAGER
│   │   ├── DOCUMENT_AUTHOR
│   │   └── DOCUMENT_REVIEWER
│   ├── TRAINING_MANAGER
│   │   └── TRAINER
│   └── AUDIT_MANAGER
│       └── AUDITOR
├── COMPLIANCE_OFFICER
└── READ_ONLY_AUDITOR

Role Permission Matrix

Role	User Mgmt	Doc Create	Doc Approve	E-Sign	Audit View	System Config	Training
SYSTEM_ADMIN	Full	Yes	Yes	Yes	Full	Full	Full
ORG_ADMIN	Org only	Yes	Yes	Yes	Org only	Org only	Full
QA_MANAGER	View	Yes	Yes	Yes	Dept only	No	Dept only
QA_REVIEWER	No	Yes	No	Yes	Own only	No	Required
DOCUMENT_AUTHOR	No	Yes	No	Yes	Own only	No	Required
DOCUMENT_REVIEWER	No	No	Yes	Yes	Own only	No	Required
COMPLIANCE_OFFICER	View	Yes	Yes	Yes	Full	No	View
VALIDATOR	No	Yes	Yes	Yes	Validation only	No	Required
READ_ONLY_AUDITOR	No	No	No	No	Full	No	No

1.2.2 Custom Role Creation

Creating a Custom Role

# Via Admin UI
Admin → Roles & Permissions → Create Custom Role

# Step 1: Role Definition
Name: "Regulatory Affairs Specialist"
Description: "Manages regulatory submissions and compliance documentation"
Role Code: "REG_AFFAIRS_SPECIALIST"
Category: "Quality & Compliance"

# Step 2: Permission Selection
Document Permissions:
  ✓ Create regulatory documents
  ✓ Edit own documents
  ✓ Submit for approval
  ✓ View approved documents
  ✗ Delete documents
  ✓ Export for regulatory submission

Audit Permissions:
  ✓ View audit trails (own actions + department)
  ✓ Generate compliance reports
  ✗ Modify audit settings

E-Signature Permissions:
  ✓ Apply electronic signature
  ✓ Witness signatures
  ✗ Override signature requirements

# Step 3: Constraints
Departments: ["Regulatory Affairs", "Quality Assurance"]
Data Access Scope: "Department + Cross-functional read"
Require Training: true
Training Courses: ["FDA Regulations Overview", "21 CFR Part 11 Compliance"]
MFA Required: true

# Step 4: Approval Workflow
Requires Approval From: "COMPLIANCE_OFFICER"
Effective Date: Immediate upon approval
Review Period: Annual

Custom Role API

POST /api/v1/roles
Authorization: Bearer {ADMIN_API_KEY}

{
  "name": "Regulatory Affairs Specialist",
  "code": "REG_AFFAIRS_SPECIALIST",
  "description": "Manages regulatory submissions",
  "permissions": {
    "documents": ["create", "edit_own", "submit", "view_approved", "export"],
    "audit": ["view_department", "generate_reports"],
    "signatures": ["apply", "witness"]
  },
  "constraints": {
    "departments": ["Regulatory Affairs", "Quality Assurance"],
    "dataScope": "department_plus_read",
    "requireTraining": true,
    "trainingCourses": ["course_fda_101", "course_part11"],
    "requireMFA": true
  },
  "approvalRequired": true,
  "reviewInterval": "annual"
}

1.2.3 Role Assignment and Inheritance

Multi-Role Assignment

Users can have multiple roles for flexibility:

# User: jane.smith@pharma.com
Assigned Roles:
  1. QA_REVIEWER (primary)
  2. DOCUMENT_AUTHOR (secondary)
  3. TRAINER (functional)

Effective Permissions: UNION of all role permissions
Audit Trail: Logs which role was active for each action
Role Switching: User can select active role context in UI

Role Inheritance Rules

inheritance_policy:
  mode: "additive"  # Permissions accumulate across roles

  conflict_resolution:
    # If roles have conflicting permissions
    rule: "most_permissive_wins"
    example:
      - ROLE_A allows "edit_all_documents"
      - ROLE_B allows "edit_own_documents"
      - Effective permission: "edit_all_documents"

  audit_logging:
    log_active_role: true
    log_permission_source: true  # Which role granted the permission

  segregation_of_duties:
    # Prevent incompatible role combinations
    prohibited_combinations:
      - ["DOCUMENT_AUTHOR", "FINAL_APPROVER"]  # Cannot author AND approve same doc
      - ["VALIDATOR", "SYSTEM_DEVELOPER"]  # Cannot validate own code
    enforcement: "strict"  # Prevent assignment at role grant time

1.3 Organization Settings

1.3.1 Organization Hierarchy Configuration

Multi-Tenant Organization Structure

Root Organization: Pharma Corp
├── Organization Unit: Clinical Operations
│   ├── Department: Clinical Data Management
│   ├── Department: Biostatistics
│   └── Department: Medical Writing
├── Organization Unit: Quality Assurance
│   ├── Department: QA Compliance
│   ├── Department: Validation
│   └── Department: Auditing
└── Organization Unit: Regulatory Affairs
    ├── Department: US Submissions
    └── Department: EU Submissions

Configuration UI Path

Admin → Organization Settings → Hierarchy Management

Actions Available:
- Create Organization Unit
- Create Department
- Move Department to different Unit
- Set Unit/Department Administrators
- Configure data access boundaries
- Set approval workflows per Unit

Organization API Structure

POST /api/v1/organizations
Authorization: Bearer {SYSTEM_ADMIN_API_KEY}

{
  "name": "Clinical Operations",
  "type": "organizational_unit",
  "parentId": "org_root_123",
  "settings": {
    "dataIsolation": "strict",  # Units cannot access each other's data
    "inheritParentPolicies": true,
    "allowCrossUnitCollaboration": false,
    "administrators": ["user_abc", "user_def"],
    "defaultApprovalWorkflow": "workflow_clinical_sop"
  },
  "departments": [
    {
      "name": "Clinical Data Management",
      "code": "CDM",
      "manager": "user_cdm_manager"
    },
    {
      "name": "Biostatistics",
      "code": "BIOSTATS",
      "manager": "user_biostats_manager"
    }
  ]
}

1.3.2 Global System Settings

System Configuration Panel

# Admin → System Settings → General

general_settings:
  organization_name: "Pharma Corp"
  timezone: "America/New_York"  # Default for all timestamps
  date_format: "YYYY-MM-DD"  # ISO 8601
  time_format: "24h"
  language: "en-US"

  # Session management
  session_timeout_minutes: 30
  session_extension_on_activity: true
  max_concurrent_sessions_per_user: 3
  force_logout_on_password_change: true

  # Document settings
  document_numbering_scheme: "auto"  # auto | manual | hybrid
  document_prefix_format: "{DOCTYPE}-{YEAR}-{SEQUENCE}"
  version_increment_rule: "major.minor.patch"

  # E-signature settings
  signature_method: "password_reconfirm"  # password_reconfirm | biometric | pki
  signature_meaning_required: true
  witness_signature_required_for: ["SOP", "Validation_Protocol"]

  # Audit trail
  audit_retention_years: 10  # Minimum 7 for FDA compliance
  audit_export_format: "JSON"  # JSON | CSV | XML
  audit_hash_algorithm: "SHA-256"

  # Compliance features
  enable_fda_part11_mode: true
  enable_hipaa_mode: true
  enable_gxp_workflows: true
  enforce_training_before_access: true

  # System availability
  maintenance_window: "Sunday 02:00-04:00 UTC"
  planned_downtime_notification_days: 7

1.3.3 Email and Notification Settings

Notification Configuration

# Admin → System Settings → Notifications

email_settings:
  smtp_host: "smtp.pharma.com"
  smtp_port: 587
  smtp_encryption: "STARTTLS"
  smtp_auth_user: "bio-qms@pharma.com"
  smtp_from_address: "BIO-QMS System <noreply@pharma.com>"

  # Email templates
  templates:
    user_invitation:
      subject: "Welcome to BIO-QMS - Account Activation"
      enabled: true

    document_approval_request:
      subject: "ACTION REQUIRED: Document Approval - {DOCUMENT_NUMBER}"
      enabled: true
      cc_roles: ["QA_MANAGER"]

    training_due:
      subject: "Training Due: {COURSE_NAME} expires in {DAYS_REMAINING} days"
      enabled: true
      reminder_days_before: [30, 14, 7, 1]

    audit_anomaly:
      subject: "ALERT: Audit Trail Anomaly Detected"
      enabled: true
      recipients: ["COMPLIANCE_OFFICER", "SYSTEM_ADMIN"]

notification_channels:
  email: true
  in_app: true
  sms: false  # Optional, requires Twilio integration

  # Notification preferences
  allow_user_opt_out: false  # Compliance notifications cannot be disabled
  digest_mode: "immediate"  # immediate | hourly | daily
  quiet_hours: "22:00-07:00 local"

1.4 SSO Setup (SAML 2.0, OIDC)

1.4.1 SAML 2.0 Configuration

Prerequisites

Identity Provider (IdP) metadata XML or URL
Admin access to IdP (Okta, Azure AD, OneLogin, etc.)
Valid SSL certificate for BIO-QMS instance
User attribute mapping requirements documented

Step-by-Step SAML Setup

# Step 1: Access SSO Configuration
Navigate to: Admin → Security → SSO Configuration → Add SAML Provider

# Step 2: Provider Details
Provider Name: "Okta Corporate SSO"
Provider Type: SAML 2.0
Entity ID: https://bio-qms.pharma.com/saml/metadata
ACS URL: https://bio-qms.pharma.com/saml/acs
Sign-On URL: https://pharma.okta.com/app/bio-qms/sso/saml

# Step 3: Upload IdP Metadata
Method 1 - Metadata URL: https://pharma.okta.com/app/exkAbc123/sso/saml/metadata
Method 2 - Upload XML file: idp-metadata.xml

# Step 4: Attribute Mapping
NameID Format: urn:oasis:names:tc:SAML:1.1:nameid-format:emailAddress

Attribute Mappings:
  Email: http://schemas.xmlsoap.org/ws/2005/05/identity/claims/emailaddress
  FirstName: http://schemas.xmlsoap.org/ws/2005/05/identity/claims/givenname
  LastName: http://schemas.xmlsoap.org/ws/2005/05/identity/claims/surname
  Department: http://schemas.xmlsoap.org/ws/2005/05/identity/claims/department
  Roles: bio-qms-roles  # Custom claim configured in IdP

# Step 5: Role Mapping (Optional but recommended)
IdP Group/Role → BIO-QMS Role
  "QA-Reviewers" → QA_REVIEWER
  "QA-Managers" → QA_MANAGER
  "Document-Authors" → DOCUMENT_AUTHOR

# Step 6: Security Settings
Sign SAML Requests: Yes
Encrypt SAML Assertions: Yes (recommended)
Require Signed Assertions: Yes
Allowed Clock Drift: 3 minutes
Session Lifetime: 8 hours

# Step 7: Just-in-Time (JIT) Provisioning
Enable JIT Provisioning: Yes  # Create users on first SSO login
Default Role for New Users: QA_REVIEWER
Require Admin Approval: No
Auto-assign to Organization: "org_main"

SAML Metadata Export

<!-- Download from: Admin → SSO Config → Export SP Metadata -->
<!-- Provide this to your IdP administrator -->

<?xml version="1.0" encoding="UTF-8"?>
<md:EntityDescriptor xmlns:md="urn:oasis:names:tc:SAML:2.0:metadata"
                     entityID="https://bio-qms.pharma.com/saml/metadata">
  <md:SPSSODescriptor AuthnRequestsSigned="true"
                      WantAssertionsSigned="true"
                      protocolSupportEnumeration="urn:oasis:names:tc:SAML:2.0:protocol">

    <md:KeyDescriptor use="signing">
      <ds:KeyInfo xmlns:ds="http://www.w3.org/2000/09/xmldsig#">
        <ds:X509Data>
          <ds:X509Certificate>
            <!-- Certificate data -->
          </ds:X509Certificate>
        </ds:X509Data>
      </ds:KeyInfo>
    </md:KeyDescriptor>

    <md:AssertionConsumerService Binding="urn:oasis:names:tc:SAML:2.0:bindings:HTTP-POST"
                                  Location="https://bio-qms.pharma.com/saml/acs"
                                  index="0" isDefault="true"/>

    <md:AttributeConsumingService index="0">
      <md:ServiceName xml:lang="en">BIO-QMS</md:ServiceName>
      <md:RequestedAttribute Name="email" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:basic" isRequired="true"/>
      <md:RequestedAttribute Name="firstName" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:basic" isRequired="true"/>
      <md:RequestedAttribute Name="lastName" NameFormat="urn:oasis:names:tc:SAML:2.0:attrname-format:basic" isRequired="true"/>
    </md:AttributeConsumingService>

  </md:SPSSODescriptor>
</md:EntityDescriptor>

1.4.2 OIDC (OpenID Connect) Configuration

OIDC Provider Setup

# Step 1: Register BIO-QMS as OIDC Client in IdP
# Obtain from IdP:
- Client ID
- Client Secret
- Issuer URL (e.g., https://auth.pharma.com)
- Authorization Endpoint
- Token Endpoint
- UserInfo Endpoint
- JWKS URI

# Step 2: Configure in BIO-QMS
Admin → Security → SSO Configuration → Add OIDC Provider

Provider Name: "Azure AD OIDC"
Client ID: abc123-def456-ghi789
Client Secret: ********** (securely stored, encrypted at rest)
Issuer URL: https://login.microsoftonline.com/{tenant-id}/v2.0
Discovery URL: https://login.microsoftonline.com/{tenant-id}/v2.0/.well-known/openid-configuration

# Auto-discovered endpoints (from .well-known):
Authorization Endpoint: {issuer}/oauth2/v2.0/authorize
Token Endpoint: {issuer}/oauth2/v2.0/token
UserInfo Endpoint: {issuer}/openid/userinfo
JWKS URI: {issuer}/discovery/v2.0/keys

# Step 3: Scopes
Requested Scopes:
  - openid (required)
  - profile
  - email
  - offline_access (for refresh tokens)

# Step 4: Callback URL
Redirect URI: https://bio-qms.pharma.com/auth/oidc/callback
(Whitelist this in IdP configuration)

# Step 5: Claims Mapping
Email Claim: email
Name Claim: name
Given Name Claim: given_name
Family Name Claim: family_name
Groups Claim: groups (for role mapping)

# Step 6: Token Validation
Validate Issuer: Yes
Validate Audience: Yes (Client ID)
Validate Signature: Yes (using JWKS)
Token Lifetime: Use IdP settings
Refresh Token Rotation: Yes

# Step 7: Security Options
PKCE: Required (S256)
State Parameter: Required (CSRF protection)
Nonce: Required
ID Token Encryption: Optional but recommended

Testing SSO Configuration

# Built-in SSO Test Tool
Admin → Security → SSO Configuration → Test Connection

Test Steps:
1. Initiate SSO login flow
2. Redirect to IdP
3. Authenticate with test user credentials
4. Validate returned assertions/claims
5. Check attribute mapping
6. Verify role assignment
7. Confirm audit log entry

Expected Result:
✓ Successful authentication
✓ User attributes correctly mapped
✓ Roles assigned per mapping rules
✓ Audit log shows: "SSO_LOGIN_SUCCESS" event
✓ Session created with correct timeout

Common Issues:
✗ Clock skew → Adjust "Allowed Clock Drift"
✗ Attribute not found → Check IdP claim configuration
✗ Invalid signature → Verify certificate/JWKS
✗ Redirect mismatch → Ensure callback URL whitelisted in IdP

1.5 API Key Management

1.5.1 API Key Creation and Permissions

Creating API Keys

# Via Admin UI
Admin → Integrations → API Keys → Create New Key

# Step 1: Key Details
Key Name: "CI/CD Pipeline Integration"
Description: "Automated document uploads from build system"
Owner: system-automation@pharma.com
Expiration: 365 days (or "No expiration" for system keys with approval)

# Step 2: Scope Selection
Scopes (OAuth 2.0 style):
  ✓ documents:read
  ✓ documents:create
  ✓ documents:upload
  ✗ documents:delete (not granted for automation)
  ✓ audit:read
  ✗ users:* (no user management for CI/CD)
  ✓ validation:execute

# Step 3: Rate Limiting
Rate Limit: 1000 requests/hour
Burst Allowance: 50 requests/minute

# Step 4: IP Allowlist (recommended)
Allowed IP Ranges:
  - 10.0.100.0/24 (internal CI/CD subnet)
  - 203.0.113.50 (backup automation server)

# Step 5: Generate Key
Generated API Key: bio_qms_live_abc123def456...xyz789
WARNING: Copy and store securely - shown only once

# API Key Format
bio_qms_{environment}_{random_32_chars}
  environment: live | test | sandbox

API Key Storage Best Practices

# DO NOT hardcode in source code
# BAD:
API_KEY = "bio_qms_live_abc123..."

# GOOD: Use environment variables
API_KEY = process.env.BIO_QMS_API_KEY

# BETTER: Use secrets management
# AWS Secrets Manager
aws secretsmanager get-secret-value --secret-id bio-qms/api-key

# HashiCorp Vault
vault kv get secret/bio-qms/api-key

# Kubernetes Secret
kubectl create secret generic bio-qms-api-key \
  --from-literal=key='bio_qms_live_...'

1.5.2 API Key Rotation

Rotation Procedure

## API Key Rotation Schedule

**Recommended Rotation Frequency:**
- Production keys: Every 90 days
- Integration/Test keys: Every 180 days
- Personal API keys: Every 60 days
- System service keys: Annual (or on compromise)

**Rotation Process:**

1. **Pre-Rotation** (1 week before)
   - Notify API key owner of upcoming expiration
   - Review current key usage via audit logs
   - Identify all systems/scripts using the key

2. **Create New Key**
   - Generate new key with identical scopes
   - Suffix with rotation date: "CI-CD-Pipeline-2026-02"
   - Set appropriate expiration

3. **Transition Period** (Dual-key overlap)
   - Deploy new key to all consuming systems
   - Keep old key active during validation
   - Monitor both keys for usage patterns
   - Duration: 48-72 hours

4. **Revocation**
   - Verify old key no longer in use (zero requests for 24h)
   - Revoke old key via Admin UI
   - Confirm revocation via test API call (should return 401)
   - Document rotation in change log

5. **Post-Rotation**
   - Archive old key identifier for audit purposes
   - Update API key inventory
   - Verify no service disruptions

Automated Rotation Script

#!/bin/bash
# api-key-rotation.sh

# Configuration
OLD_KEY_ID="key_abc123"
KEY_NAME="CI-CD Pipeline"
SCOPES="documents:read,documents:create,documents:upload,audit:read,validation:execute"
ADMIN_API_KEY="bio_qms_live_admin_xyz..."

# Create new key
NEW_KEY_RESPONSE=$(curl -X POST https://bio-qms.pharma.com/api/v1/api-keys \
  -H "Authorization: Bearer $ADMIN_API_KEY" \
  -H "Content-Type: application/json" \
  -d "{
    \"name\": \"$KEY_NAME - $(date +%Y-%m)\",
    \"scopes\": \"$SCOPES\",
    \"expirationDays\": 90,
    \"allowedIPs\": [\"10.0.100.0/24\"]
  }")

NEW_KEY=$(echo $NEW_KEY_RESPONSE | jq -r '.apiKey')

# Update secrets management system
aws secretsmanager update-secret \
  --secret-id bio-qms/ci-cd-api-key \
  --secret-string "{\"key\":\"$NEW_KEY\",\"rotatedAt\":\"$(date -u +%Y-%m-%dT%H:%M:%SZ)\"}"

# Wait for propagation (48 hours)
echo "Waiting 48 hours for new key deployment..."
sleep $((48 * 3600))

# Verify old key has no recent usage
USAGE=$(curl -s https://bio-qms.pharma.com/api/v1/api-keys/$OLD_KEY_ID/usage \
  -H "Authorization: Bearer $ADMIN_API_KEY" | jq -r '.requestsLast24h')

if [ "$USAGE" -eq 0 ]; then
  # Revoke old key
  curl -X DELETE https://bio-qms.pharma.com/api/v1/api-keys/$OLD_KEY_ID \
    -H "Authorization: Bearer $ADMIN_API_KEY"
  echo "Old key $OLD_KEY_ID revoked successfully"
else
  echo "WARNING: Old key still in use ($USAGE requests). Manual intervention required."
  exit 1
fi

1.5.3 API Key Audit and Monitoring

Audit Dashboard

Admin → Integrations → API Keys → Usage Analytics

Metrics per API Key:
- Total requests (last 24h, 7d, 30d)
- Error rate (4xx, 5xx responses)
- Top endpoints accessed
- Request sources (IP addresses)
- Last used timestamp
- Scopes utilized vs. granted
- Rate limit hit frequency

Alerting Rules:
- Key not used in 30 days → Recommend revocation
- Unusual access pattern → Security review
- Rate limit exceeded → Capacity planning
- 401 errors after key revocation → Deployment verification

1.6 Backup and Recovery

1.6.1 Backup Strategy

Backup Components

backup_scope:
  databases:
    - postgresql_primary:
        tables: all
        includes: ["audit_logs", "documents", "users", "roles", "signatures", "trainings"]
        encryption: AES-256

  file_storage:
    - document_attachments:
        path: /var/bio-qms/attachments
        format: original + metadata

    - signature_images:
        path: /var/bio-qms/signatures
        retention: permanent (regulatory requirement)

    - system_configurations:
        path: /etc/bio-qms
        includes: ["config.yaml", "ssl_certs", "saml_metadata"]

  application_state:
    - audit_trail_hash_chain:
        critical: true  # Integrity verification

    - training_records:
        regulatory: FDA Part 11
        retention_years: lifetime_of_product + 10

Backup Schedule

Backup Type	Frequency	Retention	Storage Location	RTO	RPO
Full Backup	Daily @ 02:00 UTC	90 days	S3 Glacier Deep Archive	24h	24h
Incremental Backup	Every 4 hours	30 days	S3 Standard	4h	4h
Transaction Log	Continuous (WAL)	7 days	S3 Standard-IA	1h	<1h
Audit Trail Snapshot	Hourly	1 year	S3 Standard + Glacier	1h	1h
Configuration Backup	On change + daily	180 days	S3 + Git repo	1h	24h

RTO (Recovery Time Objective): Maximum acceptable downtime RPO (Recovery Point Objective): Maximum acceptable data loss

1.6.2 Backup Execution Procedures

Automated Backup Script

#!/bin/bash
# /opt/bio-qms/scripts/backup.sh

set -euo pipefail

# Configuration
BACKUP_DIR="/mnt/backups"
TIMESTAMP=$(date +%Y%m%d_%H%M%S)
BACKUP_NAME="bio-qms-backup-$TIMESTAMP"
S3_BUCKET="s3://pharma-corp-bio-qms-backups"
PG_HOST="bio-qms-db.pharma.internal"
PG_DB="bio_qms_production"
PG_USER="backup_user"
ENCRYPTION_KEY_PATH="/etc/bio-qms/backup-encryption.key"

# Step 1: Database Backup
echo "Starting database backup..."
pg_dump -h $PG_HOST -U $PG_USER -d $PG_DB \
  --format=custom \
  --compress=9 \
  --file="$BACKUP_DIR/$BACKUP_NAME.pgdump"

# Step 2: File System Backup
echo "Backing up attachments and configurations..."
tar -czf "$BACKUP_DIR/$BACKUP_NAME-files.tar.gz" \
  /var/bio-qms/attachments \
  /var/bio-qms/signatures \
  /etc/bio-qms/config.yaml

# Step 3: Audit Trail Export (Compliance)
echo "Exporting audit trail..."
psql -h $PG_HOST -U $PG_USER -d $PG_DB -c \
  "COPY (SELECT * FROM audit_logs WHERE created_at >= NOW() - INTERVAL '24 hours') \
   TO STDOUT WITH (FORMAT CSV, HEADER)" \
  > "$BACKUP_DIR/$BACKUP_NAME-audit.csv"

# Step 4: Hash Chain Verification
echo "Verifying audit trail integrity..."
/opt/bio-qms/bin/verify-audit-chain \
  --output "$BACKUP_DIR/$BACKUP_NAME-chain-verification.json"

# Step 5: Encryption
echo "Encrypting backup..."
openssl enc -aes-256-cbc \
  -in "$BACKUP_DIR/$BACKUP_NAME.pgdump" \
  -out "$BACKUP_DIR/$BACKUP_NAME.pgdump.enc" \
  -pass file:$ENCRYPTION_KEY_PATH

# Step 6: Upload to S3
echo "Uploading to S3..."
aws s3 cp "$BACKUP_DIR/$BACKUP_NAME.pgdump.enc" "$S3_BUCKET/daily/$BACKUP_NAME.pgdump.enc" \
  --storage-class STANDARD_IA \
  --metadata "backup_type=full,timestamp=$TIMESTAMP,retention=90d"

aws s3 cp "$BACKUP_DIR/$BACKUP_NAME-files.tar.gz" "$S3_BUCKET/daily/$BACKUP_NAME-files.tar.gz"
aws s3 cp "$BACKUP_DIR/$BACKUP_NAME-audit.csv" "$S3_BUCKET/audit/$BACKUP_NAME-audit.csv" \
  --storage-class GLACIER  # Long-term regulatory retention

# Step 7: Verification
echo "Verifying backup integrity..."
aws s3api head-object --bucket pharma-corp-bio-qms-backups \
  --key "daily/$BACKUP_NAME.pgdump.enc" \
  --checksum-mode ENABLED

# Step 8: Cleanup Local Files (keep last 3 days locally)
find $BACKUP_DIR -name "bio-qms-backup-*" -mtime +3 -delete

# Step 9: Notification
echo "Backup completed successfully: $BACKUP_NAME"
curl -X POST https://bio-qms.pharma.com/api/v1/admin/backup-notifications \
  -H "Authorization: Bearer $ADMIN_API_KEY" \
  -d "{\"status\":\"success\",\"backup_name\":\"$BACKUP_NAME\",\"size_mb\":$(du -m $BACKUP_DIR/$BACKUP_NAME.pgdump.enc | cut -f1)}"

1.6.3 Restore Procedures

Restore Process

#!/bin/bash
# /opt/bio-qms/scripts/restore.sh

# CRITICAL: Only run during maintenance window or disaster recovery
# Requires: SYSTEM_ADMIN approval + Change Control documentation

set -euo pipefail

# Configuration
RESTORE_TIMESTAMP="20260217_020000"  # Backup to restore
BACKUP_NAME="bio-qms-backup-$RESTORE_TIMESTAMP"
S3_BUCKET="s3://pharma-corp-bio-qms-backups"
RESTORE_DIR="/mnt/restore"
PG_HOST="bio-qms-db.pharma.internal"
PG_DB="bio_qms_production"
PG_USER="postgres"

# Pre-flight checks
echo "=== PRE-FLIGHT CHECKS ==="
read -p "Have you obtained SYSTEM_ADMIN approval? (yes/no): " APPROVAL
if [ "$APPROVAL" != "yes" ]; then
  echo "Restore aborted. Approval required."
  exit 1
fi

read -p "Have you notified all users of system downtime? (yes/no): " NOTIFIED
if [ "$NOTIFIED" != "yes" ]; then
  echo "Restore aborted. User notification required."
  exit 1
fi

# Step 1: Stop Application Services
echo "Stopping BIO-QMS application services..."
systemctl stop bio-qms-api
systemctl stop bio-qms-worker

# Step 2: Create Current State Backup (safety)
echo "Creating safety backup of current state..."
./backup.sh --prefix "pre-restore-safety-$(date +%Y%m%d_%H%M%S)"

# Step 3: Download Backup from S3
echo "Downloading backup from S3..."
aws s3 cp "$S3_BUCKET/daily/$BACKUP_NAME.pgdump.enc" "$RESTORE_DIR/"
aws s3 cp "$S3_BUCKET/daily/$BACKUP_NAME-files.tar.gz" "$RESTORE_DIR/"

# Step 4: Decrypt Backup
echo "Decrypting backup..."
openssl enc -aes-256-cbc -d \
  -in "$RESTORE_DIR/$BACKUP_NAME.pgdump.enc" \
  -out "$RESTORE_DIR/$BACKUP_NAME.pgdump" \
  -pass file:/etc/bio-qms/backup-encryption.key

# Step 5: Verify Backup Integrity
echo "Verifying backup integrity..."
pg_restore --list "$RESTORE_DIR/$BACKUP_NAME.pgdump" > /dev/null
if [ $? -ne 0 ]; then
  echo "ERROR: Backup file corrupted!"
  exit 1
fi

# Step 6: Drop and Recreate Database (DESTRUCTIVE)
echo "WARNING: About to drop existing database!"
read -p "Type 'CONFIRM_RESTORE' to continue: " CONFIRM
if [ "$CONFIRM" != "CONFIRM_RESTORE" ]; then
  echo "Restore aborted."
  exit 1
fi

psql -h $PG_HOST -U $PG_USER -c "DROP DATABASE IF EXISTS $PG_DB;"
psql -h $PG_HOST -U $PG_USER -c "CREATE DATABASE $PG_DB;"

# Step 7: Restore Database
echo "Restoring database from backup..."
pg_restore -h $PG_HOST -U $PG_USER -d $PG_DB \
  --verbose \
  --clean \
  --if-exists \
  "$RESTORE_DIR/$BACKUP_NAME.pgdump"

# Step 8: Restore File System
echo "Restoring attachments and configurations..."
tar -xzf "$RESTORE_DIR/$BACKUP_NAME-files.tar.gz" -C /

# Step 9: Verify Audit Trail Integrity
echo "Verifying restored audit trail..."
/opt/bio-qms/bin/verify-audit-chain --full-verification
if [ $? -ne 0 ]; then
  echo "CRITICAL: Audit trail integrity check FAILED!"
  echo "DO NOT start application. Contact compliance officer immediately."
  exit 1
fi

# Step 10: Post-Restore Validation
echo "Running post-restore validation..."
/opt/bio-qms/bin/health-check --comprehensive

# Step 11: Start Services
echo "Starting BIO-QMS application services..."
systemctl start bio-qms-api
systemctl start bio-qms-worker

# Step 12: Smoke Tests
echo "Running smoke tests..."
curl -f https://bio-qms.pharma.com/api/health || (echo "API health check failed!" && exit 1)

# Step 13: Audit Log Entry
echo "Creating audit log entry for restore operation..."
psql -h $PG_HOST -U $PG_USER -d $PG_DB -c \
  "INSERT INTO audit_logs (event_type, user_id, details, timestamp) VALUES \
   ('SYSTEM_RESTORE', 'system', '{\"backup\":\"$BACKUP_NAME\",\"restored_at\":\"$(date -u +%Y-%m-%dT%H:%M:%SZ)\"}', NOW());"

# Step 14: Notifications
echo "=== RESTORE COMPLETED ==="
echo "Backup restored: $BACKUP_NAME"
echo "Notify users that system is back online."
echo "Review audit logs for any discrepancies."

# Cleanup
rm -f "$RESTORE_DIR/$BACKUP_NAME.pgdump.enc"
rm -f "$RESTORE_DIR/$BACKUP_NAME.pgdump"

Post-Restore Validation Checklist

## Post-Restore Validation

After completing a restore, verify:

- [ ] Database connection successful
- [ ] API health endpoint returns 200 OK
- [ ] User authentication working (test with multiple auth methods)
- [ ] Document retrieval functional
- [ ] Audit trail integrity verified (hash chain intact)
- [ ] E-signature validation passes
- [ ] Training records accessible
- [ ] SSO integration functional
- [ ] Scheduled jobs running (check cron/background workers)
- [ ] Email notifications working
- [ ] API keys functional
- [ ] File attachments accessible
- [ ] System logs showing no errors
- [ ] Performance metrics normal
- [ ] Backup process re-enabled

**Compliance Verification:**
- [ ] Audit log shows restore event with admin approval
- [ ] No gap in audit trail timestamps
- [ ] All regulatory-required data present
- [ ] Signatures linked to correct documents
- [ ] Training completion records intact

**User Acceptance Testing:**
- [ ] Spot-check 10 random documents for content accuracy
- [ ] Verify most recent changes present (within RPO window)
- [ ] Confirm user permissions correct
- [ ] Test document approval workflow end-to-end

1.7 Troubleshooting

1.7.1 Common Issues and Resolutions

Issue 1: Users Cannot Log In

**Symptoms:**
- Error message: "Invalid credentials" despite correct password
- Login page redirects to SSO but fails
- Account appears "locked" in admin panel

**Diagnosis Steps:**

1. Check user account status
   Admin → Users → Search for user → View status
   Expected: "Active"
   If "Locked": View lock reason (failed auth attempts, manual lock, etc.)

2. Verify authentication method
   User profile → Authentication tab
   If SSO enabled: Test SSO connection
   If local auth: Check password policy compliance

3. Review audit logs
   Admin → Audit → Filter by user email
   Look for: LOGIN_FAILED, ACCOUNT_LOCKED, PASSWORD_EXPIRED events

4. Check MFA status
   User profile → Security → MFA Status
   If MFA enabled but device lost: Admin can reset MFA

**Resolutions:**

A. Account Locked (Failed Login Attempts)
   Action: Admin → Users → {user} → Unlock Account
   Result: User can attempt login again
   Prevention: Review password policy, consider MFA

B. Password Expired
   Action: Admin → Users → {user} → Reset Password → Send reset email
   Result: User receives password reset link
   Prevention: Increase password expiration window or implement grace period

C. SSO Configuration Issue
   Action: Admin → Security → SSO → Test Connection
   Common fixes:
   - Update IdP metadata (certificates rotate)
   - Verify callback URL whitelisted in IdP
   - Check attribute mappings
   - Review IdP user group membership

D. MFA Device Lost
   Action: Admin → Users → {user} → Security → Reset MFA
   Result: User can re-enroll MFA device on next login
   Audit: MFA reset logged with admin approval

E. Account Deactivated by Mistake
   Action: Review deactivation audit log for reason
   If error: Contact SYSTEM_ADMIN for reactivation
   Note: Reactivation may require compliance officer approval

Issue 2: Audit Trail Integrity Check Failed

**Symptoms:**
- System health check reports: "Audit chain verification failed"
- Hash mismatch detected in audit log
- Cannot generate compliance reports

**CRITICALITY:** HIGH - Potential GxP compliance violation

**Immediate Actions:**

1. **DO NOT DELETE OR MODIFY AUDIT LOGS**
2. Isolate affected time range
3. Notify compliance officer immediately
4. Preserve evidence (database snapshot)
5. Initiate incident investigation

**Diagnosis:**

bash
# Run audit chain verification tool
/opt/bio-qms/bin/verify-audit-chain --detailed --range "2026-02-01 to 2026-02-17"

# Output will show:
- First hash mismatch location
- Affected records count
- Timestamp range of issue


**Root Causes:**

A. Database Clock Skew
   - Symptom: Timestamps out of sequence
   - Fix: Synchronize database server time (NTP)
   - Prevention: Monitor NTP drift

B. Manual Database Modification (VIOLATION)
   - Symptom: Records modified outside application
   - Fix: Restore from backup, investigate who/why
   - Prevention: Restrict direct DB access, enforce application-only writes

C. Backup/Restore Issue
   - Symptom: Hash chain breaks at restore point
   - Fix: Re-verify backup integrity, may need to restore from earlier backup
   - Prevention: Test restore procedures regularly

D. Software Bug
   - Symptom: Consistent pattern of failures
   - Fix: Apply software patch, report to vendor
   - Prevention: Stay current on patches

**Resolution Documentation (Required for Audits):**

Create incident report including:
- Time of detection
- Affected record range
- Root cause analysis
- Remediation steps taken
- CAPA (Corrective and Preventive Actions)
- Compliance officer sign-off

Issue 3: Document Upload Failing

**Symptoms:**
- Error: "File upload failed"
- Upload progress bar reaches 100% but document not created
- File size limits exceeded message

**Diagnosis:**

1. Check file size
   Max file size: 100 MB (configurable)
   Location: Admin → System Settings → Document Settings → Max Upload Size

2. Check file type whitelist
   Allowed types: PDF, DOCX, XLSX, PNG, JPG (configurable)
   Location: Admin → System Settings → Document Settings → Allowed File Types

3. Check storage quota
   bash
   # Check available disk space
   df -h /var/bio-qms/attachments

   # Check organization quota
   Admin → Organizations → {org} → Storage Usage


4. Review API logs
   bash
   tail -f /var/log/bio-qms/api.log | grep "upload"

   Common errors:
   - "Antivirus scan failed" → File flagged by ClamAV
   - "Storage quota exceeded" → Org limit reached
   - "Invalid file type" → MIME type mismatch


**Resolutions:**

A. File Too Large
   Option 1: Compress file (e.g., reduce PDF quality)
   Option 2: Admin increases max upload size (requires justification)
   Option 3: Split into multiple documents

B. File Type Blocked
   Action: Admin → Settings → Add file type to whitelist
   Security review: Ensure file type safe (no .exe, .scr, etc.)

C. Storage Quota Exceeded
   Action 1: Clean up old/unused documents (with approval)
   Action 2: Admin increases org quota
   Action 3: Implement document lifecycle policy (archive old docs)

D. Antivirus False Positive
   Action: Submit file for review
   Temporary: Admin can whitelist specific file hash (audit logged)

E. Network Timeout (Large Files)
   Action: Increase upload timeout setting
   Admin → System Settings → API Settings → Upload Timeout: 300 seconds

Issue 4: SSO Redirect Loop

**Symptoms:**
- User clicks "Login with SSO"
- Redirects to IdP, authenticates successfully
- Returns to BIO-QMS but immediately redirects back to IdP
- Infinite loop

**Diagnosis:**

1. Check browser cookies
   Action: Clear cookies for bio-qms.pharma.com domain
   Reason: Corrupted session cookie

2. Verify SAML/OIDC configuration
   Admin → Security → SSO → {provider} → Test Connection

   SAML specific checks:
   - RelayState parameter preserved
   - ACS URL exactly matches IdP configuration
   - Clock skew within tolerance

   OIDC specific checks:
   - Redirect URI matches exactly (case-sensitive)
   - State parameter validation enabled
   - Token expiration reasonable

3. Review IdP logs
   Check IdP admin panel for errors during assertion/token generation

4. Check session timeout settings
   If session timeout < SSO redirect time, loop can occur
   Admin → System Settings → Session Timeout: 30 minutes minimum

**Resolutions:**

A. ACS URL Mismatch (SAML)
   Issue: IdP configured with `http://` but app uses https://
   Fix: Update IdP configuration to use https://bio-qms.pharma.com/saml/acs

B. Cookie Domain Issue
   Issue: Cookie set for wrong domain
   Fix: Admin → Settings → Session Settings → Cookie Domain: .pharma.com

C. SameSite Cookie Attribute
   Issue: Browser blocking third-party cookies
   Fix: Admin → Settings → Session Settings → SameSite: None (requires HTTPS)

D. Clock Skew (SAML)
   Issue: Server time differs from IdP by > allowed drift
   Fix: Synchronize server clocks via NTP
   Workaround: Increase allowed clock drift to 5 minutes

E. IdP Session Longer Than App Session
   Issue: User authenticated at IdP but app session expired
   Fix: Align session timeouts (app timeout >= IdP timeout)

Issue 5: API Rate Limit Exceeded

**Symptoms:**
- API returns: HTTP 429 Too Many Requests
- Integration scripts fail intermittently
- "Rate limit exceeded" in response headers

**Diagnosis:**

1. Identify which API key hitting limit
   bash
   curl -I https://bio-qms.pharma.com/api/v1/documents \
     -H "Authorization: Bearer {api_key}"

   Response headers:
   X-RateLimit-Limit: 1000
   X-RateLimit-Remaining: 0
   X-RateLimit-Reset: 1645123456  # Unix timestamp


2. Review API key usage
   Admin → Integrations → API Keys → {key} → Usage Analytics
   Charts show: Requests over time, endpoint distribution, error rate

3. Check for retry loops
   Common cause: Client retries failed request immediately
   Look for: Same endpoint called repeatedly in short time window

**Resolutions:**

A. Increase Rate Limit (Justified Request)
   Action: Admin → API Keys → {key} → Edit → Rate Limit: 2000/hour
   Justification required: Business need, capacity planning done

B. Implement Exponential Backoff (Client-Side)
   python
   import time
   import requests

   def api_call_with_retry(url, headers, max_retries=5):
       for attempt in range(max_retries):
           response = requests.get(url, headers=headers)
           if response.status_code == 429:
               retry_after = int(response.headers.get('Retry-After', 60))
               wait_time = min(retry_after, 2 ** attempt)
               time.sleep(wait_time)
               continue
           return response
       raise Exception("Max retries exceeded")


C. Batch Requests
   Instead of: 100 separate API calls
   Use: 1 batch API call with array of items
   Example: POST /api/v1/documents/batch with [{...}, {...}, ...]

D. Use Webhooks Instead of Polling
   Instead of: Polling /api/v1/documents every 10 seconds
   Use: Webhook subscription for document.created events
   Admin → Integrations → Webhooks → Create Subscription

E. Implement Caching (Client-Side)
   For rarely-changing data (e.g., user list, role definitions)
   Cache TTL: 5-15 minutes
   Reduces redundant API calls

1.7.2 Support Escalation Procedures

Escalation Tiers

## Support Escalation Matrix

| Tier | Scope | Response Time | Personnel |
|------|-------|---------------|-----------|
| **L1 - User Support** | Login issues, basic navigation, password resets | 4 business hours | Help Desk |
| **L2 - System Admin** | User management, role config, SSO issues, backups | 8 business hours | System Administrators |
| **L3 - Technical Support** | API issues, integration problems, performance | 24 business hours | DevOps/Engineering |
| **L4 - Compliance Critical** | Audit trail issues, validation failures, data integrity | 2 hours | Compliance Officer + CTO |
| **L5 - Emergency** | System outage, data loss, security breach | 30 minutes | Incident Response Team |

**Escalation Triggers:**

Auto-escalate to L4 if:
- Audit trail integrity check fails
- GxP data potentially compromised
- E-signature validation errors
- Regulatory deadline at risk

Auto-escalate to L5 if:
- System unavailable for >30 minutes
- Unauthorized access detected
- Data breach suspected
- Ransomware/malware detected

**Contact Information:**

L1 - Help Desk: helpdesk@pharma.com | +1-555-0100
L2 - System Admin: bio-qms-admin@pharma.com | +1-555-0101
L3 - Technical: devops@pharma.com | +1-555-0102
L4 - Compliance: compliance-officer@pharma.com | +1-555-0103 (24/7)
L5 - Emergency: incident-response@pharma.com | +1-555-0911 (24/7)

2. Compliance Officer Guide

2.1 Audit Trail Review

Accessing Audit Logs

# Via Web UI
Navigation: Compliance → Audit Trail

Filters Available:
- Date Range: Last 24h | 7 days | 30 days | Custom range
- Event Type: All | Login | Document | E-Signature | User Mgmt | System Config
- User: Specific user or "All users"
- Organization/Department: Scope to specific org unit
- Severity: Info | Warning | Critical
- Outcome: Success | Failure | Partial

# Via API
GET /api/v1/audit-logs?start=2026-02-01&end=2026-02-17&event_type=DOCUMENT_APPROVED&user_id=user_123
Authorization: Bearer {COMPLIANCE_OFFICER_API_KEY}

Response:
{
  "total": 145,
  "records": [
    {
      "id": "audit_abc123",
      "timestamp": "2026-02-17T14:30:22.123Z",
      "event_type": "DOCUMENT_APPROVED",
      "user_id": "user_123",
      "user_name": "Jane Smith",
      "ip_address": "10.0.50.25",
      "details": {
        "document_id": "DOC-2026-00145",
        "document_title": "Manufacturing SOP v2.1",
        "approval_role": "QA_MANAGER",
        "signature_meaning": "Reviewed and Approved"
      },
      "hash": "sha256:abc123...",
      "previous_hash": "sha256:def456..."
    }
  ]
}

Audit Log Fields (FDA 21 CFR Part 11 Compliant)

Field	Description	Example	Required By
timestamp	UTC timestamp (microsecond precision)	2026-02-17T14:30:22.123456Z	Part 11.10(e)
event_type	Action performed	DOCUMENT_CREATED	Part 11.10(e)
user_id	Unique user identifier	user_abc123	Part 11.10(e)
user_name	Human-readable name	Jane Smith	Part 11.10(e)
ip_address	Source IP address	10.0.50.25	Part 11.10(e)
session_id	Session identifier	sess_xyz789	Part 11.10(e)
details	Event-specific data (JSON)	{"document_id": "DOC-123"}	Part 11.10(e)
outcome	Success/Failure	success	Part 11.10(e)
hash	Current record hash (SHA-256)	sha256:abc...	Integrity
previous_hash	Previous record hash (chain)	sha256:def...	Integrity

2.1.2 Critical Event Monitoring

High-Risk Events Requiring Review

critical_events:
  access_control_changes:
    - USER_ROLE_GRANTED
    - USER_ROLE_REVOKED
    - PERMISSION_MODIFIED
    - ADMIN_PRIVILEGE_ESCALATION
    review_frequency: Daily
    retention: Permanent

  document_lifecycle:
    - DOCUMENT_DELETED
    - DOCUMENT_RESTORED_FROM_ARCHIVE
    - VERSION_HISTORY_MODIFIED  # Should never happen
    - DOCUMENT_EXPORTED
    review_frequency: Weekly
    retention: Lifetime + 10 years

  signature_events:
    - SIGNATURE_APPLIED
    - SIGNATURE_VERIFICATION_FAILED
    - SIGNATURE_MEANING_CHANGED
    - WITNESSING_COMPLETED
    review_frequency: Real-time alerts
    retention: Permanent

  system_integrity:
    - AUDIT_TRAIL_INTEGRITY_CHECK_FAILED
    - BACKUP_FAILED
    - UNAUTHORIZED_DATABASE_ACCESS
    - SECURITY_POLICY_MODIFIED
    review_frequency: Real-time alerts (page on-call)
    retention: Permanent

  authentication:
    - FAILED_LOGIN_SPIKE  # >5 failures in 10 min
    - SSO_CONFIGURATION_CHANGED
    - MFA_DISABLED_FOR_USER
    - PASSWORD_POLICY_WEAKENED
    review_frequency: Daily
    retention: 7 years

Automated Audit Alerts

# Configure in: Compliance → Audit Alerts → Create Rule

Example Alert: Unauthorized Document Deletion Attempt

Trigger Condition:
  event_type = "DOCUMENT_DELETE_ATTEMPTED"
  AND outcome = "failure"
  AND user_role NOT IN ("QA_MANAGER", "DOCUMENT_MANAGER")

Alert Actions:
  1. Email: compliance-officer@pharma.com
  2. Slack: #compliance-alerts channel
  3. Create incident ticket
  4. Lock user account (if >3 attempts)

Alert Message Template:
  Subject: "ALERT: Unauthorized Document Deletion Attempt"
  Body:
    User: {user_name} ({user_email})
    Attempted Action: Delete document {document_id}
    Time: {timestamp}
    IP: {ip_address}
    Reason for Failure: {failure_reason}

    Action Required: Review user permissions and intent

2.1.3 Audit Trail Integrity Verification

Hash Chain Verification Process

# Manual verification command
/opt/bio-qms/bin/verify-audit-chain --range "2026-02-01 to 2026-02-17" --verbose

# Output
=== Audit Trail Integrity Verification ===
Date Range: 2026-02-01 00:00:00 UTC to 2026-02-17 23:59:59 UTC
Total Records: 45,293

Verification Steps:
[1/5] Checking timestamp sequence........................ ✓ PASS
[2/5] Verifying hash chain integrity...................... ✓ PASS
[3/5] Validating individual record hashes................. ✓ PASS
[4/5] Checking for gaps in sequence numbers............... ✓ PASS
[5/5] Comparing against backup snapshot................... ✓ PASS

Result: INTEGRITY VERIFIED
First Hash: sha256:abc123def456...
Last Hash: sha256:xyz789ghi012...
Chain Signature: sha256:final_chain_hash_abc123...

Certificate Generated: /var/bio-qms/audit-verification-2026-02-17.pdf
(Store this certificate for regulatory inspections)

Integrity Verification Schedule

Frequency	Scope	Triggered By	Output
Hourly	Last hour	Cron job	Log entry only
Daily	Last 24 hours	Automated	Email summary to compliance
Weekly	Last 7 days	Automated	PDF certificate generated
Monthly	Full month	Automated	Signed certificate + archive to immutable storage
On-Demand	Custom range	Compliance officer	PDF certificate for audits
Pre-Audit	Full system history	Audit preparation	Complete verification report

What to Do If Verification Fails

## Audit Trail Integrity Failure Response

**IMMEDIATE ACTIONS (within 1 hour):**

1. **Isolate the Issue**
   - Stop all write operations to audit log table (read-only mode)
   - Take snapshot of current database state
   - Preserve all evidence

2. **Notify Stakeholders**
   - Compliance Officer
   - Quality Assurance Director
   - CTO/IT Director
   - Legal (if data integrity compromised)

3. **Initiate Investigation**
   - Run detailed diagnostics: `/opt/bio-qms/bin/audit-diagnostics --full`
   - Identify affected record range
   - Determine root cause (clock skew, DB modification, software bug, etc.)

4. **Containment**
   - If malicious: Revoke suspect user access
   - If system error: Apply fix (time sync, software patch)
   - If backup/restore: Compare against earlier snapshots

**INVESTIGATION CHECKLIST:**

- [ ] Review database server logs for direct SQL access
- [ ] Check database user access logs (non-application users)
- [ ] Verify NTP time synchronization status
- [ ] Compare audit table schema against baseline
- [ ] Review recent software deployments/patches
- [ ] Check for unauthorized database backup/restore operations
- [ ] Interview administrators with database access
- [ ] Review physical access logs to server room (if on-prem)

**REMEDIATION:**

- If integrity can be restored: Restore from last verified backup
- If integrity cannot be restored: Document gap, explain in regulatory submissions
- Implement preventive measures (see below)

**REGULATORY REPORTING:**

- Document incident in deviation log
- Perform CAPA (Corrective and Preventive Action)
- Include in annual regulatory report (if applicable)
- Notify FDA/EMA if impacts product quality or patient safety

**PREVENTIVE MEASURES:**

- Enable database audit logging (PostgreSQL: pgAudit)
- Restrict direct database access (application-only access)
- Implement database activity monitoring (DAM) tool
- Increase audit integrity check frequency
- Deploy write-once-read-many (WORM) storage for audit logs
- Implement blockchain-based audit trail (future enhancement)

2.2 Compliance Dashboards

2.2.1 Executive Compliance Dashboard

Access: Compliance → Dashboards → Executive Overview

Key Metrics Displayed

compliance_scorecard:
  overall_compliance_score: 94.5%  # Composite score across all frameworks

  fda_part_11_compliance:
    score: 96.2%
    controls_passing: 23 / 24
    controls_at_risk: 1  # Password policy expiration warnings
    last_assessment: "2026-02-01"
    next_review_due: "2026-05-01"

  hipaa_compliance:
    score: 92.8%
    controls_passing: 38 / 41
    controls_at_risk: 3  # Encryption at rest for backups, access log review cadence
    last_assessment: "2026-01-15"
    next_review_due: "2026-04-15"

  soc2_compliance:
    score: 95.1%
    controls_passing: 64 / 67
    controls_at_risk: 3  # Incident response testing, vendor assessment updates
    last_assessment: "2025-12-10"
    next_review_due: "2026-03-10"
    type: "Type II"
    audit_period: "2025-07-01 to 2026-06-30"

audit_trail_health:
  integrity_status: "VERIFIED"
  last_verification: "2026-02-17 06:00:00 UTC"
  records_count: 1,245,089
  oldest_record: "2024-03-15"
  retention_compliant: true

training_completion:
  overall_rate: 89.2%
  overdue_trainings: 12
  expiring_within_30_days: 45
  high_risk_users_overdue: 2  # Escalate to HR

signature_compliance:
  total_signatures_30d: 1,456
  witness_signatures_30d: 234
  failed_verifications_30d: 0  # Critical: must remain 0
  average_time_to_sign: "3.2 hours"

access_control_metrics:
  active_users: 287
  users_with_privileged_access: 23
  sod_violations: 0  # Segregation of Duties
  dormant_accounts: 8  # No login >90 days, recommend deactivation

validation_status:
  iq_oq_pq_complete: true
  last_validation_date: "2025-11-20"
  next_revalidation_due: "2026-11-20"  # Annual
  open_validation_deviations: 2

Dashboard Visualization Examples

[Compliance Trend Chart - Last 12 Months]
100% ├─────────────────────────────────────────
 95% ├─●─●─●─●─●─●─●─●─●─●─●─●─  FDA Part 11
 90% ├───────────────○─○─○─○─○──  HIPAA
 85% ├─────────────────────────────────────────
 80% ├─────────────────────────────────────────
     └──────────────────────────────────────────
      Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Jan

[Training Completion by Department]
Quality Assurance    ████████████████████ 95%
Regulatory Affairs   ███████████████████  92%
Clinical Operations  ██████████████████   88%
Manufacturing        ████████████████     78% ⚠
IT                   ███████████████████  91%

[Audit Events - Last 30 Days]
Document Actions     █████████████  45,234
User Authentication  ████████       28,123
E-Signatures         ███            9,456
System Config        ██             3,234
Access Control       █              1,987

2.2.2 FDA Part 11 Compliance Dashboard

Access: Compliance → Dashboards → FDA 21 CFR Part 11

Control Monitoring

part_11_controls:

  # Subpart B - Electronic Records

  section_11_10_validation:
    name: "Validation of Systems"
    requirement: "Persons who use closed systems to create, modify, maintain, or transmit electronic records shall employ procedures and controls"
    status: COMPLIANT
    evidence:
      - IQ/OQ/PQ protocols completed (2025-11-20)
      - Validation report signed by QA
      - Change control procedures in place
      - Annual revalidation scheduled
    last_reviewed: "2026-02-01"
    next_review: "2026-05-01"

  section_11_10_a_validation:
    name: "System Validation"
    requirement: "Determine that the system is able to perform its intended function"
    status: COMPLIANT
    evidence:
      - IQ/OQ/PQ protocols completed (2025-11-20)
      - Validation report signed by QA
      - Traceability matrix linking requirements to tests
    last_reviewed: "2026-02-01"

## 2.4 HIPAA Procedures

### 2.4.1 PHI Access Monitoring

Weekly PHI access review procedure includes:
- Access pattern analysis (baseline vs. anomalies)
- After-hours access review
- Minimum necessary compliance verification
- Export/print job monitoring
- Investigation of flagged anomalies
- Weekly attestation by Privacy Officer

**Key Metrics:** Access volume, unusual patterns, bulk exports, role-appropriate access.

### 2.4.2 Breach Notification Procedure

Four-phase breach response:
1. **Detection & Containment (0-1h):** Identify breach, notify Privacy Officer, contain
2. **Investigation (1-24h):** 4-factor risk assessment, determine notification requirement
3. **Notification (within 60 days):** Individuals, HHS, media (if >500 affected)
4. **Remediation:** CAPA, technical controls, training

**Notification Requirements:**
- Individuals: Within 60 days by first-class mail or email (if opted in)
- HHS: Within 60 days via web portal (>500) or annual log (<500)
- Media: Prominent media outlets if >500 in same state/jurisdiction

## 2.5 SOC 2 Procedures

### 2.5.1 Quarterly Control Testing

SOC 2 controls tested quarterly across 9 Common Criteria (CC1-CC9):
- Sample selection (25 instances per control)
- Test execution with evidence collection
- Deficiency documentation and remediation
- Management review and sign-off

### 2.5.2 Evidence Collection

Continuous evidence collection for SOC 2 Type II audit:
- Access provisioning/deprovisioning logs
- Change management tickets
- Backup verification reports
- Security awareness training completion records
- Incident response documentation
- Vendor assessment reports

**Evidence Repository:** `compliance-evidence/soc2/{year}/{quarter}/`

## 2.6 Evidence Collection for Regulatory Submissions

### 2.6.1 Evidence Types and Sources

| Evidence Type | Source System | Retention | Format |
|---------------|---------------|-----------|--------|
| Audit Trails | PostgreSQL audit_logs table | 10 years | JSON, CSV |
| E-Signatures | Signature records with document hash | Permanent | PDF with embedded signature block |
| Training Records | Training completion database | Lifetime + 10 years | PDF certificates |
| Validation Protocols | Document repository | Lifetime + 10 years | PDF |
| Change Control | Change management system | 7 years | PDF with approval chain |
| User Access | Access control matrix + audit logs | 7 years | Excel, PDF |

### 2.6.2 Evidence Package Assembly

**Standard Evidence Package Structure:**

evidence-package-{YYYY-MM-DD}/ ├── 01-system-description/ │ ├── architecture-diagram.pdf │ ├── system-overview.pdf │ └── user-roles-matrix.xlsx ├── 02-validation-documentation/ │ ├── IQ-protocol.pdf │ ├── OQ-protocol.pdf │ ├── PQ-protocol.pdf │ └── validation-summary-report.pdf ├── 03-audit-trails/ │ ├── audit-trail-export-{date-range}.csv │ ├── integrity-verification-certificate.pdf │ └── audit-trail-description.pdf ├── 04-signatures/ │ ├── signature-log-{date-range}.xlsx │ ├── sample-signed-documents/ (10 examples) │ └── signature-controls-description.pdf ├── 05-training-records/ │ ├── training-completion-report.xlsx │ ├── course-curricula/ │ └── sample-training-certificates.pdf ├── 06-access-control/ │ ├── access-control-matrix.xlsx │ ├── role-definitions.pdf │ └── access-review-reports/ ├── 07-change-control/ │ ├── change-log-{date-range}.xlsx │ ├── sample-change-tickets.pdf │ └── change-control-procedure.pdf ├── 08-security/ │ ├── security-controls-description.pdf │ ├── encryption-certifications.pdf │ └── vulnerability-scan-reports.pdf ├── 09-business-continuity/ │ ├── backup-logs.xlsx │ ├── DR-test-results.pdf │ └── BC-DR-plan.pdf └── 10-compliance-attestations/ ├── monthly-attestations/ ├── annual-revalidation-report.pdf └── compliance-officer-certification.pdf

## 2.7 Compliance Report Generation

### 2.7.1 Executive Compliance Scorecard

**Monthly Scorecard Generation:**

```bash
Compliance → Reports → Executive Scorecard → Generate (Monthly)

# Output: PDF + Excel dashboard
# Contents:
- Overall compliance score (composite)
- FDA Part 11 status (24 controls)
- HIPAA status (Administrative, Physical, Technical safeguards)
- SOC 2 status (90 controls across CC1-CC9)
- Audit trail health metrics
- Training completion rates
- Signature compliance
- Access control metrics
- Trend charts (12-month view)
- Risk summary (open items requiring attention)

2.7.2 Regulatory Submission Reports

Pre-Audit Compliance Report:

Comprehensive report for FDA/EMA audits:

System validation status
Audit trail integrity certification
E-signature controls evidence
Training compliance
Change control summary
Deviation/CAPA log
Continuous compliance monitoring results

Report Generation: Compliance → Reports → Regulatory Submission Package

3. Validation Protocol Documentation

3.1 IQ Protocol (Installation Qualification)

3.1.1 IQ Protocol Template

# Installation Qualification Protocol
# BIO-QMS Platform

**Protocol Number:** IQ-BIO-QMS-001
**Version:** 1.0
**Effective Date:** [Date]
**System:** BIO-QMS Quality Management System
**Software Version:** [Version]

## 1. Purpose

To verify that the BIO-QMS software is installed correctly in accordance with the vendor specifications and intended use in a GxP environment.

## 2. Scope

This Installation Qualification covers:
- Software installation and configuration
- Database installation and schema verification
- Infrastructure components (application server, load balancer, storage)
- Security controls (encryption, access control, audit logging)
- Network configuration
- Backup systems
- System documentation

## 3. Responsibilities

| Role | Name | Signature | Date |
|------|------|-----------|------|
| Validation Lead | | | |
| System Administrator | | | |
| QA Reviewer | | | |
| IT Director | | | |

## 4. Prerequisites

- [ ] Hardware/infrastructure provisioned per specifications
- [ ] Network configured and tested
- [ ] SSL certificates obtained and installed
- [ ] Database server installed
- [ ] Required software dependencies installed
- [ ] User accounts created for admin/validation team
- [ ] Backup systems configured

## 5. Installation Verification Tests

### 5.1 Software Version Verification

**Objective:** Confirm correct software version installed

**Test Steps:**
1. Log into BIO-QMS admin panel
2. Navigate to: Admin → System → About
3. Record software version number

**Expected Result:** Version matches release specification document

| Component | Expected Version | Actual Version | Pass/Fail |
|-----------|------------------|----------------|-----------|
| BIO-QMS Application | v2.3.0 | | |
| PostgreSQL Database | 14.x | | |
| Node.js Runtime | 18.x LTS | | |
| Operating System | Ubuntu 22.04 LTS | | |

**Evidence:** Screenshot of version screen attached as Appendix A.

---

### 5.2 Database Schema Verification

**Objective:** Verify database schema matches specification

**Test Steps:**
1. Connect to PostgreSQL database
2. Query schema version: `SELECT version FROM schema_migrations ORDER BY version DESC LIMIT 1;`
3. Count tables: `SELECT COUNT(*) FROM information_schema.tables WHERE table_schema = 'public';`
4. Verify critical tables exist

**Expected Result:**
- Schema version: 245 (or current)
- Table count: 47
- All critical tables present

| Table Name | Expected | Present? | Pass/Fail |
|------------|----------|----------|-----------|
| users | Yes | | |
| documents | Yes | | |
| audit_logs | Yes | | |
| signatures | Yes | | |
| training_records | Yes | | |
| organizations | Yes | | |
| roles | Yes | | |

**Evidence:** Database schema export attached as Appendix B.

---

### 5.3 Infrastructure Configuration

**Objective:** Verify infrastructure components configured correctly

**Test Steps:**
1. Verify application server configuration
2. Verify database server configuration
3. Verify load balancer configuration
4. Verify storage configuration
5. Verify network/firewall rules

**Expected Result:** All components match architecture specification

| Component | Specification | Actual Configuration | Pass/Fail |
|-----------|---------------|---------------------|-----------|
| Application Server | 4 vCPU, 16 GB RAM | | |
| Database Server | 8 vCPU, 32 GB RAM | | |
| Storage | Google Cloud Storage, Standard class | | |
| Load Balancer | HTTPS only, SSL termination | | |
| Firewall | Port 443 open, all other ports closed | | |

**Evidence:** Infrastructure configuration screenshots attached as Appendix C.

---

### 5.4 Security Controls Verification

**Objective:** Verify security controls installed and configured

**Test Steps:**
1. Verify TLS/SSL configuration
2. Verify encryption at rest enabled
3. Verify audit logging enabled
4. Verify password policy configured
5. Verify session timeout configured

**Expected Result:** All security controls operational

| Security Control | Expected Configuration | Actual | Pass/Fail |
|------------------|------------------------|--------|-----------|
| TLS Version | TLS 1.3 | | |
| Certificate Validity | Valid, not expired | | |
| Database Encryption | AES-256 | | |
| Audit Logging | Enabled, all tables | | |
| Password Min Length | 12 characters | | |
| Session Timeout | 30 minutes | | |
| MFA Support | Enabled | | |

**Evidence:** Security configuration export attached as Appendix D.

---

### 5.5 System Documentation Review

**Objective:** Verify all required documentation present and current

**Test Steps:**
1. Review System Architecture Document
2. Review User Manual
3. Review Administrator Guide
4. Review API Documentation
5. Review Security Documentation

**Expected Result:** All documents present, current (within 6 months), approved

| Document | Version | Date | Approved? | Pass/Fail |
|----------|---------|------|-----------|-----------|
| System Architecture | 2.0 | | | |
| User Manual | 2.3 | | | |
| Administrator Guide | 2.3 | | | |
| API Documentation | 2.3 | | | |
| Security Controls | 1.5 | | | |

**Evidence:** Document inventory list attached as Appendix E.

---

## 6. Installation Qualification Summary

**Total Tests:** _____
**Passed:** _____
**Failed:** _____
**Pass Rate:** _____%

**Acceptance Criteria:** 100% pass rate required for IQ approval

**Deviations:**
[List any test failures or deviations from expected results, with justification/remediation plan]

**Conclusion:**

The BIO-QMS software installation [ ] DOES [ ] DOES NOT meet the Installation Qualification acceptance criteria.

---

## 7. Approvals

| Role | Name | Signature | Date |
|------|------|-----------|------|
| Validation Lead | | | |
| QA Reviewer | | | |
| IT Director | | | |

---

**Appendices:**
- Appendix A: Software Version Screenshots
- Appendix B: Database Schema Export
- Appendix C: Infrastructure Configuration
- Appendix D: Security Configuration
- Appendix E: Document Inventory

3.2 OQ Protocol (Operational Qualification)

3.2.1 OQ Protocol Template (Condensed)

Objective: Verify system operates according to functional specifications

Test Categories:

Authentication & Authorization (15 tests)
Document Management (20 tests)
E-Signature Functionality (12 tests)
Audit Trail (10 tests)
Training Management (8 tests)
Reporting (7 tests)
System Administration (10 tests)

Sample Test Cases:

TC-OQ-001: User Login with Valid Credentials

Precondition: User account exists, status = Active
Steps: Enter username/password, click Login
Expected: Successful login, redirected to dashboard
Result: [ ] Pass [ ] Fail

TC-OQ-015: Apply Electronic Signature

Precondition: User has signing authority, document in "Pending Approval" state
Steps: Open document, click Sign, enter password, enter signature meaning
Expected: Signature applied, audit log entry created, document state → "Approved"
Result: [ ] Pass [ ] Fail

Acceptance Criteria: ≥95% pass rate

3.3 PQ Protocol (Performance Qualification)

3.3.1 PQ Protocol Template (Condensed)

Objective: Demonstrate system performs as intended under realistic production conditions

Test Scenarios:

PQ-001: End-to-End Document Approval Workflow

Simulate 20 documents through complete lifecycle
Success Criteria: 100% completion, <24h average time, all signatures valid

PQ-002: Concurrent User Load

Simulate 100 concurrent users
Success Criteria: <3s page load, no errors, all actions logged

PQ-003: Audit Trail Integrity Under Load

Generate 10,000 audit events, verify integrity
Success Criteria: 100% hash chain integrity, no gaps

PQ-004: Backup and Recovery

Full backup → simulated failure → restore
Success Criteria: <2h backup, <4h restore, 100% data integrity

PQ-005: Training Compliance Workflow

50 users assigned training → completion → access granted
Success Criteria: 100% tracking accuracy, access control enforcement

3.4 Validation Execution Procedures

Validation Execution Workflow:

Pre-Execution: Protocol review, test environment preparation, test data creation
Execution: Execute tests per protocol, record results in real-time
Deviation Handling: Document failures, root cause analysis, retest
Evidence Collection: Screenshots, logs, exports for each test
Review: QA review of results, approve/reject
Sign-Off: Multi-level approval (Validation Lead, QA, IT Director)

3.5 Evidence Packaging

Validation Evidence Package:

validation-evidence-package-{YYYY-MM-DD}/
├── IQ-protocol-executed.pdf (signed)
├── IQ-evidence/
│   ├── software-version-screenshots/
│   ├── database-schema-export.sql
│   ├── infrastructure-config.yaml
│   └── security-config-export.json
├── OQ-protocol-executed.pdf (signed)
├── OQ-evidence/
│   ├── test-case-results/ (82 test cases)
│   ├── screenshots/
│   └── test-data-exports/
├── PQ-protocol-executed.pdf (signed)
├── PQ-evidence/
│   ├── performance-test-results.xlsx
│   ├── load-test-reports.pdf
│   └── scenario-execution-logs/
└── validation-summary-report.pdf (signed by QA Director)

4. Regulatory Submission Documentation

4.1 FDA CSV (Computer System Validation) Package

4.1.1 CSV Package Structure

FDA Submission Package for Computer System Validation:

FDA-CSV-Package-BIO-QMS/
├── 1-Executive-Summary.pdf
├── 2-System-Description/
│   ├── 2.1-System-Overview.pdf
│   ├── 2.2-Architecture-Diagram.pdf
│   ├── 2.3-Data-Flow-Diagram.pdf
│   ├── 2.4-User-Roles-Matrix.xlsx
│   └── 2.5-GxP-Functionality-Description.pdf
├── 3-Risk-Assessment/
│   ├── 3.1-Risk-Assessment-Report.pdf
│   ├── 3.2-Failure-Modes-Analysis.xlsx
│   └── 3.3-Risk-Mitigation-Controls.pdf
├── 4-Validation-Documentation/
│   ├── 4.1-Validation-Plan.pdf
│   ├── 4.2-IQ-Protocol-Results.pdf
│   ├── 4.3-OQ-Protocol-Results.pdf
│   ├── 4.4-PQ-Protocol-Results.pdf
│   ├── 4.5-Traceability-Matrix.xlsx
│   └── 4.6-Validation-Summary-Report.pdf
├── 5-21-CFR-Part-11-Compliance/
│   ├── 5.1-Part-11-Compliance-Matrix.xlsx
│   ├── 5.2-Audit-Trail-Description.pdf
│   ├── 5.3-E-Signature-Controls.pdf
│   ├── 5.4-Sample-Audit-Trail-Export.csv
│   └── 5.5-Sample-Signed-Documents.pdf
├── 6-SOPs-and-Procedures/
│   ├── 6.1-System-Administration-SOP.pdf
│   ├── 6.2-User-Training-SOP.pdf
│   ├── 6.3-Change-Control-SOP.pdf
│   ├── 6.4-Backup-Recovery-SOP.pdf
│   ├── 6.5-Incident-Response-SOP.pdf
│   └── 6.6-Periodic-Review-SOP.pdf
├── 7-Training-Documentation/
│   ├── 7.1-Training-Curriculum.pdf
│   ├── 7.2-Training-Completion-Records.xlsx
│   └── 7.3-Sample-Training-Certificates.pdf
├── 8-Change-Control-Log/
│   ├── 8.1-Change-Control-Procedure.pdf
│   └── 8.2-Change-Log-Since-Validation.xlsx
├── 9-Vendor-Documentation/
│   ├── 9.1-Vendor-Qualification.pdf
│   ├── 9.2-Quality-Agreement.pdf
│   ├── 9.3-Vendor-Audit-Report.pdf
│   └── 9.4-Software-Development-Lifecycle.pdf
└── 10-Appendices/
    ├── 10.1-Glossary-of-Terms.pdf
    ├── 10.2-Acronyms-and-Abbreviations.pdf
    ├── 10.3-References.pdf
    └── 10.4-Document-History.xlsx

4.2 System Description

4.2.1 GxP System Description Template

BIO-QMS System Description for Regulatory Submission:

1. System Overview

Purpose: Regulated Quality Management System for pharmaceutical/biotech
Intended Use: Document management, training, e-signatures, audit trails
Scope: GxP-regulated processes (SOPs, batch records, validation protocols)
Deployment: Cloud-based SaaS (Google Cloud Platform)

2. System Architecture

Application Layer: NestJS (Node.js), React TypeScript UI
Data Layer: PostgreSQL 14, Google Cloud Storage
Security Layer: TLS 1.3, AES-256 encryption, RBAC
Integration Layer: REST API, SAML/OIDC SSO

3. GxP Functionality

Electronic document management with version control
Electronic signatures (21 CFR Part 11 compliant)
Audit trail (secure, time-stamped, immutable)
Training management with prerequisite enforcement
Workflow engine for approval processes

4. Data Classification

Critical GxP Data: Approved SOPs, batch records, validation protocols
PHI/PII: Clinical trial documents (HIPAA-regulated)
Audit Data: Complete system audit trail (FDA Part 11 requirement)

5. User Roles

System Admin, QA Manager, QA Reviewer, Document Author, Validator, Compliance Officer, Auditor

4.3 Risk Assessment

4.3.1 GxP Risk Assessment

Risk Assessment Methodology: FMEA (Failure Modes and Effects Analysis)

Risk Categories:

Data Integrity Risks
Audit Trail Risks
E-Signature Risks
Access Control Risks
System Availability Risks

Sample Risk:

Risk ID	Risk Description	Impact	Likelihood	Risk Level	Mitigation Control
R-001	Audit trail data corruption	High	Low	Medium	Hash chain integrity verification (hourly)
R-002	Unauthorized access to GxP data	High	Low	Medium	RBAC + MFA + audit logging
R-003	E-signature not linked to correct document	High	Very Low	Low	Foreign key constraints + document hash at signature time
R-004	System unavailability during critical operation	Medium	Low	Low	99.9% SLA + automated failover + backup systems

4.4 Validation Summary

Validation Summary Report:

System: BIO-QMS v2.3.0
Validation Type: Prospective Validation
Validation Date: [Date]
Validation Team: [Names and roles]

Results:

IQ: 25/25 tests passed (100%)
OQ: 82/82 tests passed (100%)
PQ: 5/5 scenarios passed (100%)
Overall: System VALIDATED for GxP use

Conclusion: BIO-QMS meets all regulatory requirements for use in GxP-regulated environments.

4.5 EU Annex 11 Submissions

4.5.1 Annex 11 Compliance Matrix

EU GMP Annex 11 - Computerised Systems Compliance:

Clause	Requirement	Compliance	Evidence
1. Risk Management	Risk assessment of computerised systems	Compliant	Risk assessment report (Section 4.3)
4. Validation	Validation documentation	Compliant	IQ/OQ/PQ protocols (Section 3)
9. Audit Trail	Secure, computer-generated audit trail	Compliant	Audit trail hash chain + integrity verification
10. Change Control	Formal change control procedures	Compliant	Change control SOP + change log
12. Security	Physical and logical security	Compliant	Access control matrix + encryption
15. Backup	Regular backup with tested restore	Compliant	Automated daily backups + quarterly DR tests

Submission Format: EU CTD (Common Technical Document) Module 3.2.P.3.5 (if applicable to product submissions)

Summary

This comprehensive Admin & Compliance Documentation covers:

✅ F.3.1 System Administrator Guide - User management, SSO, backups, troubleshooting (Sections 1.1-1.7) ✅ F.3.2 Compliance Officer Guide - Audit review, dashboards, FDA/HIPAA/SOC2 procedures (Sections 2.1-2.7) ✅ F.3.3 Validation Protocol Documentation - IQ/OQ/PQ templates and execution (Sections 3.1-3.5) ✅ F.3.4 Regulatory Submission Documentation - FDA CSV package, EU Annex 11, risk assessments (Sections 4.1-4.5)

Document Stats:

Total Length: ~3,000 lines (2,900+ markdown lines)
Compliance Frameworks: FDA 21 CFR Part 11, HIPAA, SOC 2, EU Annex 11
Protocol Templates: 3 complete (IQ, OQ, PQ)
Procedures: 15+ SOPs and checklists
Evidence Structures: 4 comprehensive packaging templates

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Document Purpose​

Table of Contents​

1. System Administrator Guide

1.1 User Management​

1.1.1 User Lifecycle Management​

1.1.2 Password Policy Configuration​

1.1.3 User Deactivation Process​

1.2 Role Configuration​

1.2.1 Built-in Roles​

1.2.2 Custom Role Creation​

1.2.3 Role Assignment and Inheritance​

1.3 Organization Settings​

1.3.1 Organization Hierarchy Configuration​

1.3.2 Global System Settings​

1.3.3 Email and Notification Settings​

1.4 SSO Setup (SAML 2.0, OIDC)​

1.4.1 SAML 2.0 Configuration​

1.4.2 OIDC (OpenID Connect) Configuration​

1.5 API Key Management​

1.5.1 API Key Creation and Permissions​

1.5.2 API Key Rotation​

1.5.3 API Key Audit and Monitoring​

1.6 Backup and Recovery​

1.6.1 Backup Strategy​

1.6.2 Backup Execution Procedures​

1.6.3 Restore Procedures​

1.7 Troubleshooting​

1.7.1 Common Issues and Resolutions​

1.7.2 Support Escalation Procedures​

2. Compliance Officer Guide

2.1 Audit Trail Review​

2.1.1 Audit Trail Access and Navigation​

2.1.2 Critical Event Monitoring​

2.1.3 Audit Trail Integrity Verification​

2.2 Compliance Dashboards​

2.2.1 Executive Compliance Dashboard​

2.2.2 FDA Part 11 Compliance Dashboard​

2.7.2 Regulatory Submission Reports​