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#

System TypeGAMP CategoryDocumentsEDC (Electronic Data Capture)Category 4/5All 12 documentsCTMS (Clinical Trial Management)Category 4VP, URS, FS, RA, IQ, OQ, RTMLIMS (Laboratory Information Management)Category 4/5All 12 documentsMES (Manufacturing Execution System)Category 4All 12 documentsERP (Enterprise Resource Planning)Category 4VP, URS, RA, IQ, OQSCADA/DCSCategory 2/3VP, URS, IQ, OQ, PQCustom SoftwareCategory 3/4VP, URS, RA, IQ, OQ

Quick Start#

bash

# 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)#

bash

# 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:

text

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#

CommandDescriptionOutput Formatgenerate.py vpValidation Plan.docxgenerate.py ursUser Requirements Specification.docxgenerate.py fsFunctional Specification.docxgenerate.py tsTechnical Specification.docxgenerate.py raRisk Assessment (FMEA).docxgenerate.py iqInstallation Qualification.docxgenerate.py oqOperational Qualification.docxgenerate.py pqPerformance Qualification.docxgenerate.py rtmTraceability Matrix.xlsxgenerate.py vsrValidation Summary Report.docxgenerate.py checklistValidation Checklist.xlsxgenerate.py test-caseTest Case Template.xlsxgenerate.py allFull validation package.docx / .xlsx

Command Options#

OptionDescriptionRequired--projectProject nameYes--systemSystem name and versionYes--categoryGAMP category (1-5). If not specified, interactive selection will be prompted with bilingual GAMP 5 guidance.No (will prompt)--bilingualEnable bilingual mode: 'true' or 'false' (default: true). When true, headers remain bilingual and content follows --language.No--languagePrimary language for content: 'zh' (Chinese) or 'en' (English) (default: zh). Used when bilingual=false or for content in bilingual mode.No--verbose / -vShow detailed progress information (default: simplified output)No--outputOutput directoryYes--formatOutput format: docx, xlsx, or both (default: both)No

Output Format Standards#

All generated documents follow consistent naming and formatting rules:

Document Naming Convention#

Document TypeFormatExampleValidation Plan{TYPE}_{PROJECT}.{ext}VP_XX系统.docxUser Requirements{TYPE}_{PROJECT}.{ext}URS_XX系统.docxFunctional Specification{TYPE}_{PROJECT}.{ext}FS_XX系统.docxTraceability MatrixRTM_{PROJECT}.{ext}RTM_XX系统.xlsx

Output Directory Structure#

text

{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:

VariableDescriptionExample{PROJECT_NAME}Project name临床试验系统{SYSTEM_NAME}System nameEDC v1.0{SYSTEM_VERSION}System version1.0{GAMP_CATEGORY}GAMP category4{DOC_ID}Document IDURS-001{DATE}Document date2024-01-01{AUTHOR}Document author张三{REVIEWER}Reviewer name李四{APPROVER}Approver name王五

Regulatory Compliance#

GAMP 5 Categories#

CategoryDescriptionValidation Approach1Operating SystemLegacy2FirmwareSimplified3Commercial-off-the-shelf (COTS)Risk-based4Configured COTSRisk-based5Custom/CriticalFull validation

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#

text

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#

ActionDescriptionPre-conditionsparse_requirements()Parse @URS, @FS, @TEST markers from source codeSource code availablegenerate_vp()Create Validation PlanProject name, system name, GAMP categorygenerate_urs()Create User Requirements SpecificationSystem context, GxP scopegenerate_fs()Create Functional SpecificationURS requirements linkedgenerate_ra()Create Risk AssessmentURS priorities, GxP scopegenerate_iq_oq_pq()Create Qualification ProtocolsRA risk levels, TS configgenerate_rtm()Create Traceability MatrixURS, FS, test cases linkedgenerate_vsr()Create Validation Summary ReportAll test results, deviationssync_bidirectional()Sync requirements ↔ templatesTemplates and requirements.json existrun_compliance_check()Verify GxP complianceRequirements and test results

Data Flow Semantics#

FlowSemantic MeaningVP → URSBusiness process analysis defines GxP scope for requirementsURS → FSFunctional requirements trace to design specificationsURS → RARequirement priority determines risk severityRA → TestRisk level scales testing rigor (IQ/OQ/PQ scope)All → RTMComplete 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:

FileDescriptiongamp-5.mdGAMP 5 quick reference guide21cfr-part11.md21 CFR Part 11 key requirementsannex-11.mdEU Annex 11 requirementsdata-integrity.mdALCOA+ data integrity principles

Example Templates#

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

Example FileDescriptionurs-example.mdURS with complete requirement examplesfs-example.mdFS with traceability examplesra-example.mdRA with hierarchical risk examplesiq-example.mdIQ 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``--languageBehaviortrue (default)zhHeaders bilingual, content in Chinesetrue (default)enHeaders bilingual, content in Englishfalse``zhPure Chinese outputfalse``enPure English output

Bilingual Template Format#

Templates use dual-language format for headers:

markdown

## 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#

text

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:

python

# @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:

PatternExampleDescription// @REQ URS-xxx``// @REQ URS-001 - 系统应支持RBACRequirement 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-001FS reference// @TS``// @TS TS-001TS reference// @RISK [H/M/L]``// @RISK HRisk level (High/Medium/Low)

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#

Module ID中文名English NameTest Prefixuser_mgmt用户管理User ManagementUMaudit_trail审计追踪Audit TrailATdata_mgmt数据管理Data ManagementDMbusiness_func业务功能Business FunctionsBFreporting报告功能ReportingRPintegration接口集成IntegrationINTsecurity安全SecuritySECcompliance合规ComplianceCMP

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:

text

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}

TypeExampleDescriptionIQIQ-UM-001Installation Qualification testOQOQ-UM-001Operational Qualification testPQPQ-UM-001Performance Qualification test

Auto-Sync Feature#

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

bash

# 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:

bash

# 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:

bash

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

Interactive workflow:

text

[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:

bash

# 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:

bash

# 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:

bash

# 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:

bash

# 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:

bash

# 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):

bash

# 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:

bash

# 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):

yaml

- 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):

yaml

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:

bash

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#

bash

# 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#

IssueSolutionpython-docx not installedRun: pip install -r requirements.txtEncoding errorsEnsure UTF-8 encoding in your terminalTemplate not foundCheck you are in the correct directory

Getting Help#

Run with verbose output:

bash

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:

bash

# 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#

bash

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#

bash

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#

bash

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/