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:

Supported Systems

| System Type | GAMP Category | Documents | |-------------|---------------|-----------| | EDC (Electronic Data Capture) | Category 4/5 | All 12 documents | | CTMS (Clinical Trial Management) | Category 4 | VP, URS, FS, RA, IQ, OQ, RTM | | LIMS (Laboratory Information Management) | Category 4/5 | All 12 documents | | MES (Manufacturing Execution System) | Category 4 | All 12 documents | | ERP (Enterprise Resource Planning) | Category 4 | VP, URS, RA, IQ, OQ | | SCADA/DCS | Category 2/3 | VP, URS, IQ, OQ, PQ | | Custom Software | Category 3/4 | VP, URS, RA, IQ, OQ |

Quick Start

# Navigate to skill directory
cd /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 /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 | Description | Output Format | |---------|-------------|---------------| | generate.py vp | Validation Plan | .docx | | generate.py urs | User Requirements Specification | .docx | | generate.py fs | Functional Specification | .docx | | generate.py ts | Technical Specification | .docx | | generate.py ra | Risk Assessment (FMEA) | .docx | | generate.py iq | Installation Qualification | .docx | | generate.py oq | Operational Qualification | .docx | | generate.py pq | Performance Qualification | .docx | | generate.py rtm | Traceability Matrix | .xlsx | | generate.py vsr | Validation Summary Report | .docx | | generate.py checklist | Validation Checklist | .xlsx | | generate.py test-case | Test Case Template | .xlsx | | generate.py all | Full validation package | .docx / .xlsx |

Command Options

| Option | Description | Required | |--------|-------------|----------| | --project | Project name | Yes | | --system | System name and version | Yes | | --category | GAMP category (1-5). If not specified, interactive selection will be prompted with bilingual GAMP 5 guidance. | No (will prompt) | | --bilingual | Enable bilingual mode: 'true' or 'false' (default: true). When true, headers remain bilingual and content follows --language. | No | | --language | Primary language for content: 'zh' (Chinese) or 'en' (English) (default: zh). Used when bilingual=false or for content in bilingual mode. | No | | --verbose / -v | Show detailed progress information (default: simplified output) | No | | --output | Output directory | Yes | | --format | Output format: docx, xlsx, or both (default: both) | No |

Output Format Standards

All generated documents follow consistent naming and formatting rules:

Document Naming Convention

| Document Type | Format | Example | |--------------|--------|---------| | Validation Plan | {TYPE}_{PROJECT}.{ext} | VP_XX系统.docx | | User Requirements | {TYPE}_{PROJECT}.{ext} | URS_XX系统.docx | | Functional Specification | {TYPE}_{PROJECT}.{ext} | FS_XX系统.docx | | Traceability Matrix | RTM_{PROJECT}.{ext} | RTM_XX系统.xlsx |

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:

Colors:

Template Variables

Common variables used in templates:

| Variable | Description | Example | |----------|-------------|---------| | {PROJECT_NAME} | Project name | 临床试验系统 | | {SYSTEM_NAME} | System name | EDC v1.0 | | {SYSTEM_VERSION} | System version | 1.0 | | {GAMP_CATEGORY} | GAMP category | 4 | | {DOC_ID} | Document ID | URS-001 | | {DATE} | Document date | 2024-01-01 | | {AUTHOR} | Document author | 张三 | | {REVIEWER} | Reviewer name | 李四 | | {APPROVER} | Approver name | 王五 |

Regulatory Compliance

GAMP 5 Categories

| Category | Description | Validation Approach | |----------|-------------|-------------------| | 1 | Operating System | Legacy | | 2 | Firmware | Simplified | | 3 | Commercial-off-the-shelf (COTS) | Risk-based | | 4 | Configured COTS | Risk-based | | 5 | Custom/Critical | Full validation |

Key Regulatory Requirements

This skill includes compliance checks for:

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

| Action | Description | Pre-conditions | |--------|-------------|---------------| | parse_requirements() | Parse @URS, @FS, @TEST markers from source code | Source code available | | generate_vp() | Create Validation Plan | Project name, system name, GAMP category | | generate_urs() | Create User Requirements Specification | System context, GxP scope | | generate_fs() | Create Functional Specification | URS requirements linked | | generate_ra() | Create Risk Assessment | URS priorities, GxP scope | | generate_iq_oq_pq() | Create Qualification Protocols | RA risk levels, TS config | | generate_rtm() | Create Traceability Matrix | URS, FS, test cases linked | | generate_vsr() | Create Validation Summary Report | All test results, deviations | | sync_bidirectional() | Sync requirements ↔ templates | Templates and requirements.json exist | | run_compliance_check() | Verify GxP compliance | Requirements and test results |

Data Flow Semantics

| Flow | Semantic Meaning | |------|-----------------| | VP → URS | Business process analysis defines GxP scope for requirements | | URS → FS | Functional requirements trace to design specifications | | URS → RA | Requirement priority determines risk severity | | RA → Test | Risk level scales testing rigor (IQ/OQ/PQ scope) | | All → RTM | Complete traceability matrix for regulatory audit |

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:

| File | Description | |------|-------------| | gamp-5.md | GAMP 5 quick reference guide | | 21cfr-part11.md | 21 CFR Part 11 key requirements | | annex-11.md | EU Annex 11 requirements | | data-integrity.md | ALCOA+ data integrity principles |

Example Templates

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

| Example File | Description | |--------------|-------------| | urs-example.md | URS with complete requirement examples | | fs-example.md | FS with traceability examples | | ra-example.md | RA with hierarchical risk examples | | iq-example.md | IQ with qualification check examples |

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 | --language | Behavior | |---------------|--------------|----------| | true (default) | zh | Headers bilingual, content in Chinese | | true (default) | en | Headers bilingual, content in English | | false | zh | Pure Chinese output | | false | en | Pure English output |

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:

| 中文 | English | |------|---------| | 验证计划 | Validation Plan | | 用户需求 | User Requirements |

Content cells use format like 中文 / English:

| 模块 / Module | 描述 / Description | |--------------|-------------------| | 用户管理 / User Management | 系统应... / System should... |

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:

| Pattern | Example | Description | |---------|---------|-------------| | // @REQ URS-xxx | // @REQ URS-001 - 系统应支持RBAC | Requirement with ID and description | | # @REQ | # @REQ URS-001 - 描述 | Python-style comment | | /* @REQ */ | /* @REQ URS-001 - 描述 */ | Multi-line comment | | // @TEST[type-id] | // @TEST[OQ-UM-001] - 验证 | Test case link | | // @FS | // @FS FS-001 | FS reference | | // @TS | // @TS TS-001 | TS reference | | // @RISK [H/M/L] | // @RISK H | Risk level (High/Medium/Low) |

Risk levels:

Standard Modules

| Module ID | 中文名 | English Name | Test Prefix | |-----------|--------|--------------|-------------| | user_mgmt | 用户管理 | User Management | UM | | audit_trail | 审计追踪 | Audit Trail | AT | | data_mgmt | 数据管理 | Data Management | DM | | business_func | 业务功能 | Business Functions | BF | | reporting | 报告功能 | Reporting | RP | | integration | 接口集成 | Integration | INT | | security | 安全 | Security | SEC | | compliance | 合规 | Compliance | CMP |

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}

| Type | Example | Description | |------|---------|-------------| | IQ | IQ-UM-001 | Installation Qualification test | | OQ | OQ-UM-001 | Operational Qualification test | | PQ | PQ-UM-001 | Performance Qualification test |

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:

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:

Exit codes:

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:

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:

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:

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:

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 /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

| Issue | Solution | |-------|----------| | python-docx not installed | Run: pip install -r requirements.txt | | Encoding errors | Ensure UTF-8 encoding in your terminal | | Template not found | Check you are in the correct directory |

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/

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/

Common Issues

| Issue | Solution | |-------|----------| | python-docx not installed | Run: pip install -r requirements.txt | | Encoding errors | Ensure UTF-8 encoding in your terminal | | Template not found | Check you are in the correct directory |

Getting Help

Run with verbose output:

python3 scripts/generate.py --help