CSV Documentation Generator

CSV Documentation Generator

Generate Computerized System Validation (CSV) documentation for pharmaceutical and medical device industries. Supports bilingual (Chinese/English) templates and multiple output formats (Word/Excel).

When to Use

Use this skill when:

• Creating validation documentation for GMP-regulated systems
• Generating User Requirements Specification (URS) with regulatory compliance checks
• Preparing IQ/OQ/PQ protocols for system qualification
• Creating traceability matrices linking requirements to test cases
• Conducting risk assessments for computerised systems
• Need documentation templates that comply with GAMP 5, 21 CFR Part 11, EU Annex 11

Supported Systems

Quick Start

# Navigate to skill directory
cd <SKILL_DIR>/csv-documentation-generator

# Run script - will automatically create virtual environment on first run
python3 scripts/generate.py vp --project "XX系统" --system "EDC v1.0" --output ./output/

# Note: If --category is not specified, interactive GAMP category selection will be prompted
# The script provides bilingual (Chinese/English) guidance based on GAMP 5 Second Edition

# Generate Validation Plan (with category specified)
python3 scripts/generate.py vp --project "XX系统" --system "EDC v1.0" --category 4 --output ./output/

# Generate full validation package
python3 scripts/generate.py all --project "XX系统" --system "MES" --category 4 --output ./validation/

Parse Requirements from Code (pre-generation)

# Navigate to skill directory
cd <SKILL_DIR>/csv-documentation-generator

# Parse source code for requirements (extracts @URS, @TEST, @FS, @TS markers)
python3 scripts/cli.py parse ./src

# For AI agents (non-interactive mode), use --auto-add:
python3 scripts/cli.py parse ./src --auto-add

# Review extracted requirements
cat requirements.json

Auto Environment Setup

This skill automatically handles environment setup:

1. First run: Automatically creates .venv virtual environment in skill directory
2. Dependencies: Automatically installs required packages (python-docx, openpyxl, etc.)
3. Subsequent runs: Use the already-created virtual environment

This ensures consistent behavior and avoids dependency conflicts.

Interactive GAMP Category Selection

If --category is not specified, the script will prompt with bilingual (Chinese/English) guidance:

GAMP 5 (Second Edition) Category Selection:
  [1] Infrastructure Software - 基础设施软件
  [2] Firmware - 固件
  [3] Commercial Off-The-Shelf (COTS) - Non-configured - 商用现货软件 (不可配置)
  [4] Configured COTS - 配置型 COTS 软件 (e.g., EDC, CTMS, LIMS, MES)
  [5] Custom / Critical Application - 定制/关键应用

AI agents should guide users to select the appropriate category based on GAMP 5 Second Edition principles.

Available Commands

Command Options

Output Format Standards

All generated documents follow consistent naming and formatting rules:

Document Naming Convention

Output Directory Structure

{output_dir}/
├── VP_项目名.docx
├── URS_项目名.docx
├── FS_项目名.docx
├── TS_项目名.docx
├── RA_项目名.docx
├── IQ_项目名.docx
├── OQ_项目名.docx
├── PQ_项目名.docx
├── VSR_项目名.docx
├── RTM_项目名.xlsx
└── CHECKLIST_项目名.xlsx

Document Styling Standards

Fonts:

• Chinese text: SimSun (宋体)
• English text: Arial

Colors:

• Table headers: #2563EB (Royal Blue) with white text
• Priority markers: [必须] (red), [应该] (amber), [可以] (green)
• Test results: [通过] (green), [失败] (red), [待测] (amber)

Template Variables

Common variables used in templates:

Regulatory Compliance

GAMP 5 Categories

Key Regulatory Requirements

This skill includes compliance checks for:

• 21 CFR Part 11: Electronic Records and Signatures

  • Audit trail requirements
  • Electronic signature requirements
  • System access controls

• EU Annex 11: Computerised Systems

  • Validation requirements
  • Data integrity
  • Change control

• ALCOA+: Data Integrity

  • Attributable
  • Legible
  • Contemporaneous
  • Original
  • Accurate (+ Complete, Consistent, Enduring)

Semantic Action Graph

This skill encapsulates the following semantic actions for GxP document generation:

Action Graph

parse_requirements(source_path) → RequirementsDB
    │
    ▼
generate_vp(context) → Document
    │ ──────────────────────► generate_urs(context) → Document
    │                                           │
    │ ◄── (URS traceability) ──────────────────┤
    │                                           ▼
    ├────────────────────────────────────► generate_fs(context) → Document
    │                                           │
    │ ◄── (FS technical specs) ─────────────────┤
    │                                           ▼
    └────────────────────────────────────► generate_ra(context) → Document
                                                    │
                                        ┌───────────┴───────────┐
                                        ▼                       ▼
                              generate_iq_oq_pq(context)   generate_rtm(context)
                                        │                       │
                                        └───────────┬───────────┘
                                                    ▼
                                        generate_vsr(context) → Document

Semantic Actions

Data Flow Semantics

Prompt Library

Critical Thinking Constraints and Content Fill Prompts are defined in prompts.md.

For GAMP 5 M12 Critical Thinking constraints, document generation triggering conditions, and content fill prompt templates, see prompts.md.

Reference Documents

Reference materials included in references/ folder:

Example Templates

Complete fill examples are provided in templates/examples/ directory:

AI agents SHOULD reference these examples for content style guidance when filling templates.

Bilingual Format

All templates support Smart Bilingual output controlled by --bilingual and --language flags:

Bilingual Template Format

Templates use dual-language format for headers:

## 1. 目的 / Purpose

本文档定义了... / This document defines...

Tables use dual-language headers:

Content cells use format like 中文 / English:

Requirements Traceability

This skill supports GAMP 5 compliant requirements traceability across the entire validation lifecycle.

Automated Traceability Chain

代码注释 (@URS[module]) 
    ↓
requirements.json (需求解析)
    ↓
URS 模板 (自动同步章节)
    ↓
FS/TS 文档 (引用需求ID)
    ↓
测试用例 (关联需求ID)
    ↓
测试结果 (解析需求ID)
    ↓
RTM (追溯矩阵自动生成)

Code Comment Standards (AI Agent Must Follow)

When generating code, AI agents MUST include requirement markers for automatic traceability. Use the standardized @REQ format:

# @REQ URS-001 - 系统应支持基于角色的访问控制 (RBAC)
# @REQ URS-002 - 用户密码必须满足复杂度要求（至少8位）
# @FS FS-001
# @TS TS-001
# @TEST[OQ-UM-001] - 验证用户角色分配功能
# @RISK H  # High risk module

def assign_role(user_id: str, role: str) -> bool:
    '''
    @REQ URS-001 - Role-based access control required
    @TEST[OQ-UM-001] - Test role assignment
    '''
    # Implementation...

Standard comment formats:

Risk levels:

• H (High): Security, compliance, electronic signature, audit trail related
• M (Medium): Default for most requirements
• L (Low): Simple features, documentation, reports

Standard Modules

注意: 章节号（4.X）是动态分配的，基于模板中已有的章节。同步时会自动为新模块分配下一个可用编号。

System Prompt Integration (Manual Configuration Required)

⛔ This step is NOT automatic. You must manually add these rules to your agent's system prompt (AGENTS.md) if you want @REQ/@TEST annotations to apply across ALL skills.

To enable cross-skill annotation enforcement, add the following to your AGENTS.md or agent system prompt:

Code Annotation Rules (for GxP traceability):
- When writing code that implements requirements, add @REQ markers: # @REQ URS-xxx - description
- When writing test cases, add @TEST markers: # @TEST[OQ-UM-xxx] - description
- Mark high-risk code sections with @RISK H (security, compliance, audit trail related)
- Mark medium-risk code with @RISK M
- Mark low-risk code with @RISK L

Why this is needed: OpenClaw skills only execute when active. There is no mechanism to make instructions persist across skill switches except via the system prompt.

See STANDARDS.md for full documentation and standards/code-annotations.json for the standards file.

Test Case ID Format

Test case IDs follow the format: {IQ|OQ|PQ}-{ModulePrefix}-{Number}

Auto-Sync Feature

Before generating documents, use --sync to automatically update templates with new requirements:

# Generate URS and sync requirements to template
python3 scripts/generate.py urs --sync \
  --project "临床系统" \
  --system "EDC v1.0" \
  --category 4 \
  --output ./validation/

# Generate full validation package with sync
python3 scripts/generate.py all --sync \
  --project "XX系统" \
  --system "MES" \
  --category 4 \
  --output ./validation/

What --sync does:

1. Reads requirements.json for all requirements
2. Groups requirements by module
3. Checks if each module section exists in template
4. Auto-appends new module sections if missing
5. Backs up original template before modification

Sync Template to Database

Use --sync-template-to-db to extract requirements from templates and add them to requirements.json:

# Extract requirements from urs.md template to requirements.json
python3 scripts/generate.py urs --sync-template-to-db \
  --project "临床系统" \
  --system "EDC v1.0" \
  --category 4 \
  --output ./validation/

What --sync-template-to-db does:

1. Reads the template (e.g., urs.md)
2. Extracts all requirements in | URS-xxx | description | format
3. Loads existing requirements.json (if exists)
4. Adds new requirements that don't already exist
5. Preserves existing requirements and test results

Interactive Mode

For interactive step-by-step document generation with confirmation prompts:

python3 scripts/generate.py all --interactive \
  --project "临床系统" \
  --system "EDC v1.0" \
  --category 4 \
  --output ./validation/

Interactive workflow:

[1/11] 解析代码注释...
  → 按 Enter 继续，'s' 跳过，'q' 退出:

[2/11] 同步需求到数据库...
  → 按 Enter 继续，'s' 跳过，'q' 退出:

[3/11] 生成 URS...
  → 按 Enter 继续，'s' 跳过，'q' 退出:
  ✓ ./output/URS_临床系统.docx
...

Options:

• Enter - Execute this step
• s - Skip this step
• q - Quit (already generated files are preserved)

Compliance Check

Run GAMP 5 compliance validation to check requirements coverage and test coverage:

# Run compliance check (text output)
python3 scripts/generate.py check \
  --requirements requirements.json \
  --test-results test_results.json

# Run compliance check (JSON output for CI/CD)
python3 scripts/generate.py check \
  --requirements requirements.json \
  --test-results test_results.json \
  --output-format json

Compliance checks performed:

• Requirement coverage (ensures all code requirements are documented)
• High-risk module verification (IQ/OQ/PQ tests for critical modules)
• Test coverage threshold (default 80%)

Exit codes:

• 0 - All checks passed
• 1 - Warnings present
• 2 - Errors found

Incremental Update (Smart Rebuild)

Use --diff-only to skip regeneration when requirements haven't changed:

# Only regenerate RTM if requirements changed
python3 scripts/generate.py rtm --diff-only \
  --project "临床系统" \
  --system "EDC v1.0" \
  --category 4 \
  --output ./validation/

How it works:

1. Computes SHA256 hash of requirements after each generation
2. Stores hash in .requirements.hash in output directory
3. On subsequent runs, compares current hash against stored hash
4. Skips generation if hash matches (requirements unchanged)

Git Hooks (Automated Compliance)

Install post-commit hooks to automatically run compliance checks after code commits:

# Install hooks locally (per-project)
./scripts/git-hooks/install.sh --local

# Install hooks globally (all projects)
./scripts/git-hooks/install.sh --global

# Uninstall hooks
./scripts/git-hooks/install.sh --uninstall

What the hook does:

• Detects commits with code or requirements changes
• Runs compliance check (non-blocking)
• Outputs warnings to stderr without blocking commit

Bidirectional Sync

Use --sync for bidirectional sync between template and requirements.json:

# Full bidirectional sync (both directions)
python3 scripts/generate.py urs --sync \
  --project "临床系统" \
  --system "EDC v1.0" \
  --category 4

# Only sync template → JSON
python3 scripts/generate.py urs --sync --sync-direction to-json

# Only sync JSON → template
python3 scripts/generate.py urs --sync --sync-direction to-template

Conflict resolution:

# Keep template descriptions on conflict
python3 scripts/generate.py urs --sync --conflict-resolution template

# Keep JSON descriptions on conflict
python3 scripts/generate.py urs --sync --conflict-resolution json

# Keep newer version based on updated_at
python3 scripts/generate.py urs --sync --conflict-resolution newer

Section numbering behavior:

• Sync automatically creates module sections with ### 4.X headers
• Section numbers are dynamically assigned based on existing sections in the template
• Only modules with requirements in requirements.json will have sections created
• Custom modules (e.g., pm_query, multi_lock) are supported and will be assigned the next available section number

Monorepo Support

For projects with multiple subprojects (monorepo structure):

# Auto-detect monorepo root
python3 scripts/generate.py rtm --project "临床系统" --system "EDC v1.0"

# Explicitly specify monorepo root
python3 scripts/generate.py rtm --project "临床系统" --system "EDC v1.0" \
  --project-root /path/to/monorepo

Detected monorepo layouts:

• apps/, packages/, projects/, modules/, services/ directories
• Each subproject with its own requirements.json

Template Versioning

Templates are versioned for compatibility tracking:

# Check compatibility (automatic on generate)
python3 scripts/generate.py rtm --project "系统" --system "v1.0" --category 4

# Specify template version
python3 scripts/generate.py rtm --template-version 1.2.0 \
  --project "系统" --system "v1.0" --category 4

Automatic migrations:

• Templates are automatically migrated to current version
• Version checks prevent incompatible generator/template combinations

CI/CD Integration

Use provided CI/CD templates for automated documentation generation:

GitHub Actions (templates/ci/github-actions.yml):

- uses: actions/checkout@v4
- uses: actions/setup-python@v5
  with:
    python-version: '3.11'
- run: pip install -r requirements.txt
- run: python scripts/generate.py check --output-format json
- run: python scripts/generate.py all --diff-only

GitLab CI (templates/ci/gitlab-ci.yml):

generate:rtm:
  extends: .csv-docs-base
  script:
    - python scripts/generate.py rtm --diff-only
  artifacts:
    paths:
      - validation/RTM*.xlsx

Important Notes

Template Requirements Are Examples

The URS/FS/TS IDs and descriptions in templates are examples only. For actual projects:

1. Review and modify template requirements based on real system needs
2. Delete or replace example requirements as appropriate
3. Use --sync-template-to-db to populate initial requirements, then customize

Change-Driven Risk Assessment (GxP)

Per GxP requirements, any system change requires a risk assessment. When generating RA documents, include the change description:

python3 scripts/generate.py ra \
  --project "临床系统" \
  --system "EDC v1.0" \
  --change-description "升级数据库从 v12 到 v14" \
  --output ./validation/

Parsing Requirements from Code

# Navigate to skill directory
cd <SKILL_DIR>/csv-documentation-generator

# Parse source code for requirements using csv-docs CLI
python3 scripts/cli.py parse ./src

# View extracted requirements
cat requirements.json

Troubleshooting

Common Issues

Getting Help

Run with verbose output:

python3 scripts/generate.py --help

Examples

AI Agent (Non-Interactive Mode)

For AI agents running in non-interactive mode, use --auto-add to automatically add all parsed requirements:

# Parse and auto-add all requirements (non-interactive)
python3 scripts/cli.py parse ./src --auto-add

# Generate with verbose output
python3 scripts/generate.py all --project "XX系统" --system "System v1.0" --category 4 --verbose

Example 1: Generate URS for CTMS

python3 scripts/generate.py urs \
  --project "临床试验管理系统" \
  --system "CTMS v2.0" \
  --category 4 \
  --bilingual true \
  --output ./validation/

Example 2: Generate Risk Assessment

python3 scripts/generate.py ra \
  --project "质量管理系统" \
  --system "QMS v1.5" \
  --category 4 \
  --critical-functions "数据录入,审计追踪,权限控制" \
  --output ./validation/

Example 3: Generate Traceability Matrix

python3 scripts/generate.py rtm \
  --project "实验室系统" \
  --system "LIMS v3.0" \
  --category 4 \
  --urs-file ./URS-001.md \
  --fs-file ./FS-001.md \
  --output ./validation/