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.

# 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

```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:

```
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:**
- 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:

| 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:

- **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) ─────────────────┤
    │