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csv-documentation-generator Use when generating computer system validation (CSV) documentation for pharmaceutical and medical device industries, including validation plans, URS, FS, IQ/OQ/PQ documents, and traceability matrices.
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.csv-docs-config.json 1.6 KB name csv-documentation-generator description Use when generating computer system validation (CSV) documentation for pharmaceutical and medical device industries, including validation plans, URS, FS, IQ/OQ/PQ documents, and traceability matrices. triggers ["Generate CSV documentation","创建 GMP 验证文档","计算机化系统验证","IQ OQ PQ protocol","URS FS RA 追溯矩阵","GAMP 5 validation","GxP","21 CFR Part 11","电子签名","电子记录","EDC","CTMS","eTMF","LIMS","医疗器械"] category gxp-compliance version 1.6.4 author zealot00 homepage https://github.com/zealot00/csv-documentation-generator repository https://github.com/zealot00/csv-documentation-generator bugs https://github.com/zealot00/csv-documentation-generator/issues createdAt 2026-03-18 lastReviewedAt 2026-03-18 validationStatus beta compatibility {"openclaw":">=1.0.0","python":">=3.10"} requiredTools ["exec","write"] inputSchema {"type":"object","required":["project","system"],"properties":{"docType":{"type":"string","enum":["vp","urs","fs","ra","iq","oq","pq","rtm","vsr","checklist","test-case","all"]},"project":{"type":"string","description":"项目名称 / Project name"},"system":{"type":"string","description":"系统名称及版本 / System name and version"},"category":{"type":"integer","enum":[1,2,3,4,5],"description":"GAMP category (1-5)"},"bilingual":{"type":"boolean","default":true},"output":{"type":"string","default":"./output"}}} outputSchema {"type":"object","properties":{"docx":{"type":"array","items":{"type":"string"},"description":"Generated Word documents"},"xlsx":{"type":"array","items":{"type":"string"},"description":"Generated Excel documents"}}}
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 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
cd <SKILL_DIR>/csv-documentation-generator
python3 scripts/generate.py vp --project "XX系统" --system "EDC v1.0" --output ./output/
python3 scripts/generate.py vp --project "XX系统" --system "EDC v1.0" --category 4 --output ./output/
"XX系统"
"MES"
Parse Requirements from Code (pre-generation)
cd <SKILL_DIR>/csv-documentation-generator
python3 scripts/cli.py parse ./src
python3 scripts/cli.py parse ./src --auto-add
cat requirements.json
Auto Environment Setup This skill automatically handles environment setup:
First run : Automatically creates .venv virtual environment in skill directoryDependencies : Automatically installs required packages (python-docx, openpyxl, etc.)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 vpValidation Plan .docx generate.py ursUser Requirements Specification .docx generate.py fsFunctional Specification .docx generate.py tsTechnical Specification .docx generate.py raRisk Assessment (FMEA) .docx generate.py iqInstallation Qualification .docx generate.py oqOperational Qualification .docx generate.py pqPerformance Qualification .docx generate.py rtmTraceability Matrix .xlsx generate.py vsrValidation Summary Report .docx generate.py checklistValidation Checklist .xlsx generate.py test-caseTest Case Template .xlsx generate.py allFull validation package .docx / .xlsx
Command Options Option Description Required --projectProject name Yes --systemSystem name and version Yes --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 directory Yes --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 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
Chinese text: SimSun (宋体)
English text: Arial
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:
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.mdGAMP 5 quick reference guide 21cfr-part11.md21 CFR Part 11 key requirements annex-11.mdEU Annex 11 requirements data-integrity.mdALCOA+ data integrity principles
Example Templates Complete fill examples are provided in templates/examples/ directory:
Example File Description urs-example.mdURS with complete requirement examples fs-example.mdFS with traceability examples ra-example.mdRA with hierarchical risk examples iq-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--languageBehavior true (default)zhHeaders bilingual, content in Chinese true (default)enHeaders bilingual, content in English falsezhPure Chinese output falseenPure 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:
def assign_role (user_id: str , role: str ) -> bool :
'''
@REQ URS-001 - Role-based access control required
@TEST[OQ-UM-001] - Test role assignment
'''
Standard comment formats:
Pattern Example Description // @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)
H (High): Security, compliance, electronic signature, audit trail relatedM (Medium): Default for most requirementsL (Low): Simple features, documentation, reports
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.
Test Case ID Format Test case IDs follow the format: {IQ|OQ|PQ}-{ModulePrefix}-{Number}
Type Example Description IQ IQ-UM-001Installation Qualification test OQ OQ-UM-001Operational Qualification test PQ PQ-UM-001Performance Qualification test
Auto-Sync Feature Before generating documents, use --sync to automatically update templates with new requirements:
python3 scripts/generate.py urs --sync \
--project "临床系统" \
--system "EDC v1.0" \
--category 4 \
--output ./validation/
python3 scripts/generate.py all --sync \
--project "XX系统" \
--system "MES" \
--category 4 \
--output ./validation/
Reads requirements.json for all requirements
Groups requirements by module
Checks if each module section exists in template
Auto-appends new module sections if missing
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:
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:
Reads the template (e.g., urs.md)
Extracts all requirements in | URS-xxx | description | format
Loads existing requirements.json (if exists)
Adds new requirements that don't already exist
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/
[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
...
Enter - Execute this steps - Skip this stepq - Quit (already generated files are preserved)
Compliance Check Run GAMP 5 compliance validation to check requirements coverage and test coverage:
python3 scripts/generate.py check \
--requirements requirements.json \
--test-results test_results.json
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%)
0 - All checks passed1 - Warnings present2 - Errors found
Incremental Update (Smart Rebuild) Use --diff-only to skip regeneration when requirements haven't changed:
python3 scripts/generate.py rtm --diff-only \
--project "临床系统" \
--system "EDC v1.0" \
--category 4 \
--output ./validation/
Computes SHA256 hash of requirements after each generation
Stores hash in .requirements.hash in output directory
On subsequent runs, compares current hash against stored hash
Skips generation if hash matches (requirements unchanged)
Git Hooks (Automated Compliance) Install post-commit hooks to automatically run compliance checks after code commits:
./scripts/git-hooks/install.sh --local
./scripts/git-hooks/install.sh --global
./scripts/git-hooks/install.sh --uninstall
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:
python3 scripts/generate.py urs --sync \
--project "临床系统" \
--system "EDC v1.0" \
--category 4
python3 scripts/generate.py urs --sync --sync-direction to-json
python3 scripts/generate.py urs --sync --sync-direction to-template
python3 scripts/generate.py urs --sync --conflict-resolution template
python3 scripts/generate.py urs --sync --conflict-resolution json
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):
python3 scripts/generate.py rtm --project "临床系统" --system "EDC v1.0"
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/ directoriesEach subproject with its own requirements.json
Template Versioning Templates are versioned for compatibility tracking:
python3 scripts/generate.py rtm --project "系统" --system "v1.0" --category 4
python3 scripts/generate.py rtm --template-version 1.2.0 \
--project "系统" --system "v1.0" --category 4
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:
Review and modify template requirements based on real system needs
Delete or replace example requirements as appropriate
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
cd <SKILL_DIR>/csv-documentation-generator
python3 scripts/cli.py parse ./src
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 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:
python3 scripts/cli.py parse ./src --auto-add
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/
